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BMRB: 30139

5KVP

Solution structure of the catalytic domain of zoocin A

Authors

Timkovich, R., Xing, M., Simmonds, R.S.

Assembly

Zoocin A endopeptidase

Entity

1. Zoocin A endopeptidase, entity 1 (polymer, Thiol state: not present), 159 monomers, 16833.50 Da Detail

MRGSHHHHHH GSATYTRPLD TGNITTGFNG YPGHVGVDYA VPVGTPVRAV ANGTVKFAGN GANHPWMLWM AGNAVLIQHA DGMHTGYAHL SKISVSTDST VKQGQIIGYT GATGQVTGPH LHFEMLPANP NWQNGFSGRI DPTGYIANAP VFNGTTPTE

2. Zoocin A endopeptidase, entity ZN (non-polymer), 65.409 Da
3. Zoocin A endopeptidase, entity UNL (non-polymer), na Da

Total weight

16898.908 Da

Max. entity weight

16833.5 Da

Source organism

Streptococcus equi subsp. zooepidemicus

Exptl. method

solution NMR

Refine. method

SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.9 %, Completeness: 84.8 %, Completeness (bb): 94.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.8 % (1461 of 1722)	84.5 % (739 of 875)	82.9 % (564 of 680)	94.6 % (158 of 167)
Backbone	94.0 % (876 of 932)	93.3 % (308 of 330)	94.5 % (429 of 454)	93.9 % (139 of 148)
Sidechain	77.0 % (713 of 926)	79.1 % (431 of 545)	72.7 % (263 of 362)	100.0 % (19 of 19)
Aromatic	24.7 % (46 of 186)	46.2 % (43 of 93)	0.0 % (0 of 90)	100.0 % (3 of 3)
Methyl	100.0 % (162 of 162)	100.0 % (81 of 81)	100.0 % (81 of 81)

1. entity 1

MRGSHHHHHH GSATYTRPLD TGNITTGFNG YPGHVGVDYA VPVGTPVRAV ANGTVKFAGN GANHPWMLWM AGNAVLIQHA DGMHTGYAHL SKISVSTDST VKQGQIIGYT GATGQVTGPH LHFEMLPANP NWQNGFSGRI DPTGYIANAP VFNGTTPTE

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 297 K, pH 5.6, Details 10 mM potassium phosphate, 0.1 mM sodium azide, 1.1 mM [U-95% 13C; U-90% 15N] Protein, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 297 K, pH 5.6, Details 10 mM potassium phosphate, 0.1 mM sodium azide, 0.5 mM [U-95% 13C; U-90% 15N] protein, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 297 K, pH 5.6, Details 10 mM potassium phosphate, 0.1 mM sodium azide, 1.0 mM [U-90% 15N] protein, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	potassium phosphate	natural abundance	10 mM
8	protein	[U-90% 15N]	1.0 mM
9	sodium azide	natural abundance	0.1 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	na	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	na	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	na	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	na	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.31 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5KVP, Strand ID: A Detail

Release date

2016-10-23

Citation

Solution structure of the Cys74 to Ala74 mutant of the recombinant catalytic domain of Zoocin A
Xing, M., Simmonds, R.S., Timkovich, R.
Proteins (2016), 85, 177-181, PubMed 27699884 , DOI 10.1002/prot.25178 , Abstract

Related entities 1. Zoocin A endopeptidase, entity 1, : 1 : 1 entities Detail

Experiments performed 26 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 297 K, pH 5.6, Details 10 mM potassium phosphate, 0.1 mM sodium azide, 1.1 mM [U-95% 13C; U-90% 15N] Protein, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

2 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

5 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

7 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

10 3D CCC-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

11 3D HCC-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

12 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 297 K, pH 5.6, Details 10 mM potassium phosphate, 0.1 mM sodium azide, 0.5 mM [U-95% 13C; U-90% 15N] protein, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

13 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

14 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

15 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

16 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

17 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

18 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

19 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

20 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

21 3D CCC-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

22 3D HCC-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

23 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 297 K, pH 5.6, Details 10 mM potassium phosphate, 0.1 mM sodium azide, 1.0 mM [U-90% 15N] protein, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	potassium phosphate	natural abundance	10 mM
8	protein	[U-90% 15N]	1.0 mM
9	sodium azide	natural abundance	0.1 mM

24 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	potassium phosphate	natural abundance	10 mM
8	protein	[U-90% 15N]	1.0 mM
9	sodium azide	natural abundance	0.1 mM

25 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Protein	[U-95% 13C; U-90% 15N]	1.1 mM
2	potassium phosphate	natural abundance	10 mM
3	sodium azide	natural abundance	0.1 mM

26 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
4	potassium phosphate	natural abundance	10 mM
5	protein	[U-95% 13C; U-90% 15N]	0.5 mM
6	sodium azide	natural abundance	0.1 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30139_5kvp.nef
Input source #2: Coordindates	5kvp.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:34:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:38:ASP:OD1	2:1:ZN:ZN	unknown	unknown	n/a
1:38:ASP:OD2	2:1:ZN:ZN	unknown	unknown	n/a
1:122:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
2:1:ZN:ZN	3:1:UNL:O	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	UNL	Unknown ligand	None
C	1	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MRGSHHHHHHGSATYTRPLDTGNITTGFNGYPGHVGVDYAVPVGTPVRAVANGTVKFAGNGANHPWMLWMAGNAVLIQHADGMHTGYAHLSKISVSTDST
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MRGSHHHHHHGSATYTRPLDTGNITTGFNGYPGHVGVDYAVPVGTPVRAVANGTVKFAGNGANHPWMLWMAGNAVLIQHADGMHTGYAHLSKISVSTDST

-------110-------120-------130-------140-------150---------
VKQGQIIGYTGATGQVTGPHLHFEMLPANPNWQNGFSGRIDPTGYIANAPVFNGTTPTE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VKQGQIIGYTGATGQVTGPHLHFEMLPANPNWQNGFSGRIDPTGYIANAPVFNGTTPTE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	159	0	0	100.0

Content subtype: combined_30139_5kvp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	Warning	5		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1463		95.6 (chain: A, length: 159)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3269 (1)	noe	92.5 (chain: A, length: 159)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	32 (1)	noe	10.1 (chain: A, length: 159)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	54 (1)	hbond	18.9 (chain: A, length: 159)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_7	OK	262 (262)	.	90.6 (chain: A, length: 159)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 95.6%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MRGSHHHHHHGSATYTRPLDTGNITTGFNGYPGHVGVDYAVPVGTPVRAVANGTVKFAGNGANHPWMLWMAGNAVLIQHADGMHTGYAHLSKISVSTDST
 ||      |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
.RG......HGSATYTRPLDTGNITTGFNGYPGHVGVDYAVPVGTPVRAVANGTVKFAGNGANHPWMLWMAGNAVLIQHADGMHTGYAHLSKISVSTDST

-------110-------120-------130-------140-------150---------
VKQGQIIGYTGATGQVTGPHLHFEMLPANPNWQNGFSGRIDPTGYIANAPVFNGTTPTE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VKQGQIIGYTGATGQVTGPHLHFEMLPANPNWQNGFSGRIDPTGYIANAPVFNGTTPTE

Total number of assignments
- ¹H chemical shifts: 728
- ¹³C chemical shifts: 575
- ¹⁵N chemical shifts: 160

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
23	ASN	CG	177.08
29	ASN	CG	177.01
52	ASN	CG	176.26
60	ASN	CG	177.2
63	ASN	CG	177.33
73	ASN	CG	176.3
78	GLN	CD	179.81
79	HIS	HD1	10.99
79	HIS	ND1	165.0
103	GLN	CD	180.0
105	GLN	CD	179.45
115	GLN	CD	179.7
129	ASN	CG	177.78
131	ASN	CG	177.34
133	GLN	CD	180.65
134	ASN	CG	178.6
148	ASN	CG	177.67
153	ASN	CG	177.2

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	875	727	83.1
¹³C chemical shifts	680	559	82.2
¹⁵N chemical shifts	171	159	93.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	330	309	93.6
¹³C chemical shifts	318	301	94.7
¹⁵N chemical shifts	148	137	92.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	545	418	76.7
¹³C chemical shifts	362	258	71.3
¹⁵N chemical shifts	23	22	95.7

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	84	97.7
¹³C chemical shifts	86	83	96.5

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	93	37	39.8
¹³C chemical shifts	90	0	0.0
¹⁵N chemical shifts	3	3	100.0

Peptide bond of PRO
Tautomeric state of HIS
Rotameric state of ILE , LEU, and VAL
Histogram of normalized assigned chemical shifts
Random coil index and derived parameters (S² and NMR RMSD)
- Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: Warning

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 92.5%
- Total number of restraints: 3255
- Weight of restraints: 1.0 (3255)
- Potential type of restraints: square-well-parabolic (3255)
- Range of distance target values: 2.1, 3.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 10.1%
  - Total number of restraints: 31
  - Weight of restraints: 1.0 (31)
  - Potential type of restraints: square-well-parabolic (31)
  - Range of distance target values: 2.75, 3.25 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
    - Chain_ID: C
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 18.9%
    - Total number of restraints: 54
    - Weight of restraints: 1.0 (54)
    - Potential type of restraints: square-well-parabolic (54)
    - Range of distance target values: 2.05, 2.95 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
      - Chain_ID: C
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 90.6%
- Total number of restraints: 262
- Total number of restraints per polymer type: 262
- Weight of restraints: 1.0 (262)
- Potential type of restraints: square-well-parabolic (262)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords anti-microbial, endopeptidase, exoenzyme, hydrolase

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Found 1 Document (0.601 seconds)

BMRB: 30139

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Zoocin A endopeptidase, entity 1, : 1 : 1 entities Detail

Experiments performed 26 experiments Detail

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