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BMRB: 34077

5MNW

Solution structure of the cinaciguat bound human beta1 H-NOX.

Authors

Matzapetakis, M., Saraiva, I.H.

Assembly

Guanylate cyclase soluble subunit beta-1 (E.C.4.6.1.2)

Entity

1. Guanylate cyclase soluble subunit beta-1 (E.C.4.6.1.2), entity 1 (polymer), 194 monomers, 22429.20 Da Detail

MYGFVNHALE LLVIRNYGPE VWEDIKKEAQ LDEEGQFLVR IIYDDSKTYD LVAAASKVLN LNAGEILQMF GKMFFVFCQE SGYDTILRVL GSNVREFLQN LDALHDHLAT IYPGMRAPSF RCTDAEKGKG LILHYYSERE GLQDIVIGII KTVAQQIHGT EIDMKVIQQR NEECDHTQFL IEEKESKEHH HHHH

2. Guanylate cyclase soluble subunit beta-1 (E.C.4.6.1.2), entity Z90 (non-polymer), 565.699 Da

Total weight

22994.898 Da

Max. entity weight

22429.2 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 32.5 %, Completeness: 19.5 %, Completeness (bb): 24.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	19.5 % (451 of 2318)	18.6 % (224 of 1202)	19.0 % (172 of 906)	26.2 % (55 of 210)
Backbone	24.3 % (281 of 1158)	24.6 % (98 of 398)	22.7 % (129 of 569)	28.3 % (54 of 191)
Sidechain	15.7 % (210 of 1341)	15.7 % (126 of 804)	16.0 % (83 of 518)	5.3 % (1 of 19)
Aromatic	9.3 % (20 of 214)	11.2 % (12 of 107)	7.5 % (8 of 106)	0.0 % (0 of 1)
Methyl	20.1 % (45 of 224)	19.6 % (22 of 112)	20.5 % (23 of 112)

1. entity 1

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 1 mM [U-99% 13C; U-99% 15N] beta1 H-NOX, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

Chem. Shift Complete2

Sequence coverage: 91.8 %, Completeness: 29.4 %, Completeness (bb): 40.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	29.4 % (1362 of 4636)	26.4 % (635 of 2404)	26.9 % (487 of 1812)	57.1 % (240 of 420)
Backbone	40.5 % (938 of 2316)	40.6 % (323 of 796)	34.3 % (390 of 1138)	58.9 % (225 of 382)
Sidechain	18.9 % (507 of 2682)	19.4 % (312 of 1608)	17.4 % (180 of 1036)	39.5 % (15 of 38)
Aromatic	10.0 % (43 of 428)	13.6 % (29 of 214)	6.1 % (13 of 212)	50.0 % (1 of 2)
Methyl	26.1 % (117 of 448)	27.2 % (61 of 224)	25.0 % (56 of 224)

1. entity 1

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM [U-99% 13C; U-99% 15N] beta1 H-NOX, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

Chem. Shift Complete3

Sequence coverage: 94.8 %, Completeness: 45.8 %, Completeness (bb): 57.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	45.8 % (3185 of 6954)	42.6 % (1536 of 3606)	44.7 % (1216 of 2718)	68.7 % (433 of 630)
Backbone	57.4 % (1993 of 3474)	57.4 % (685 of 1194)	53.1 % (906 of 1707)	70.2 % (402 of 573)
Sidechain	35.8 % (1439 of 4023)	35.3 % (851 of 2412)	35.8 % (557 of 1554)	54.4 % (31 of 57)
Aromatic	22.6 % (145 of 642)	29.6 % (95 of 321)	15.1 % (48 of 318)	66.7 % (2 of 3)
Methyl	48.1 % (323 of 672)	48.8 % (164 of 336)	47.3 % (159 of 336)

1. entity 1

Show sample condition

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.81 ppm	internal	indirect	0.2514495
¹H	water	protons	4.81 ppm	internal	direct	1.0
¹⁵N	water	protons	4.81 ppm	internal	indirect	0.1013291

Referencing offset: -0.12 ppm, Outliers: 4 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.81 ppm	internal	indirect	0.2514495
¹H	water	protons	4.81 ppm	internal	direct	1.0
¹⁵N	water	protons	4.81 ppm	internal	indirect	0.1013291

Referencing offset: -0.12 ppm, Outliers: 4 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.81 ppm	internal	indirect	0.2514495
¹H	water	protons	4.81 ppm	internal	direct	1.0
¹⁵N	water	protons	4.81 ppm	internal	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.81 ppm	internal	indirect	0.2514495
¹H	water	protons	4.81 ppm	internal	direct	1.0
¹⁵N	water	protons	4.81 ppm	internal	indirect	0.1013291

Referencing offset: 0.18 ppm, Outliers: 1 Detail

Release date

2017-01-12

Citation

Solution structure of the cinaciguat bound human beta1 H-NOX
Matzapetakis, M., Saraiva, I.H.

Related entities 1. Guanylate cyclase soluble subunit beta-1 (E.C.4.6.1.2), entity 1, : 1 : 12 : 52 entities Detail

Interaction partners 1. Guanylate cyclase soluble subunit beta-1 (E.C.4.6.1.2), entity 1, : 4 interactors Detail

More details for 4 interactors identified by 2 citations

Experiments performed 17 experiments Detail

1 2D 1H-13C HSQC

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM [U-99% 13C; U-99% 15N] beta1 H-NOX, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

2 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

3 3D HNCO

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

4 3D (H)CCH-TOCSY

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

5 3D HNCA

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

6 3D 1H-13C NOESY

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

7 3D 1H-15N NOESY

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

8 3D CBCA(CO)NH

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

9 3D HNCACB

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

10 3D HN(CA)CO

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

11 H[C]_H{[c(0)]+[n(0)]}.through-space

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

12 H[c(0)]_H[c(0)].through-space

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

13 H_H{[n(0)]+[c(0)]}.through-space

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

14 H[c(0)]_H[c(0)].relayed

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

15 3D HN(COCA)HA

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

16 2D 1H-1H NOESY

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

17 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 1 mM [U-99% 13C; U-99% 15N] beta1 H-NOX, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	beta1 H-NOX	[U-99% 13C; U-99% 15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34077_5mnw.nef
Input source #2: Coordindates	5mnw.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	None
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)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	Z90	4-({(4-carboxybutyl)[2-(2-{[4-(2-phenylethyl)benzyl]oxy}phenyl)ethyl]amino}methyl)benzoic acid	Assigned chemical shifts, Distance restraints

Sequence alignments

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

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

-------110-------120-------130-------140-------150-------160-------170-------180-------190----
LDALHDHLATIYPGMRAPSFRCTDAEKGKGLILHYYSEREGLQDIVIGIIKTVAQQIHGTEIDMKVIQQRNEECDHTQFLIEEKESKEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LDALHDHLATIYPGMRAPSFRCTDAEKGKGLILHYYSEREGLQDIVIGIIKTVAQQIHGTEIDMKVIQQRNEECDHTQFLIEEKESKEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	194	0	0	100.0

Content subtype: combined_34077_5mnw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	20		100.0 (chain: B, length: 1)
2	Assigned chemical shifts	assigned_chemical_shifts_2	Warning	547		87.6 (chain: A, length: 194)
3	Assigned chemical shifts	assigned_chemical_shifts_3	Warning	1765		93.8 (chain: A, length: 194)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	4108 (1)	noe	92.8 (chain: A, length: 194), 100.0 (chain: B, length: 1)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	265 (265)	.	75.3 (chain: A, length: 194)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 20
- Completeness of assignments
  - Entity_assemble_ID: B
Saveframe: assigned_chemical_shifts_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 194, Sequence coverage: 87.6%
- Total number of assignments
  - ¹H chemical shifts: 197
  - ¹³C chemical shifts: 173
  - ¹⁵N chemical shifts: 177
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID
1	Z90

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
99	GLN	CD	180.577

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1202	197	16.4
¹³C chemical shifts	906	172	19.0
¹⁵N chemical shifts	218	177	81.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	398	168	42.2
¹³C chemical shifts	388	165	42.5
¹⁵N chemical shifts	191	163	85.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	804	29	3.6
¹³C chemical shifts	518	7	1.4
¹⁵N chemical shifts	27	14	51.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	117	5	4.3
¹³C chemical shifts	117	6	5.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	1	0.9
¹³C chemical shifts	106	0	0.0
¹⁵N chemical shifts	1	1	100.0

Saveframe: assigned_chemical_shifts_3

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 194, Sequence coverage: 93.8%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLNLNAGEILQMFGKMFFVFCQESGYDTILRVLGSNVREFLQN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||   ||||||||||||
MYGFVNHALELLVIRNYGPEVWEDIKKEAQLDEEGQFLVRIIYDDSKTYDLVAAASKVLNLNAGEILQMFGKMFFVFCQESGYDT...VLGSNVREFLQN
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140-------150-------160-------170-------180-------190----
LDALHDHLATIYPGMRAPSFRCTDAEKGKGLILHYYSEREGLQDIVIGIIKTVAQQIHGTEIDMKVIQQRNEECDHTQFLIEEKESKEHHHHHH
||||   | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||     
LDAL...L.TIYPGMRAPSFRCTDAEKGKGLILHYYSEREGLQDIVIGIIKTVAQQIHGTEIDMKVIQQRNEECDHTQFLIEEKESKEH     
-------110-------120-------130-------140-------150-------160-------170-------180---------

Total number of assignments
- ¹H chemical shifts: 860
- ¹³C chemical shifts: 717
- ¹⁵N chemical shifts: 188

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
16	ASN	CG	176.758
30	GLN	CD	181.362
48	THR	HG1	5.67
56	SER	HG	5.195
60	ASN	CG	178.47
62	ASN	CG	176.57
68	GLN	CD	179.572
93	ASN	CG	175.359
99	GLN	CD	180.407
100	ASN	CG	177.348
143	GLN	CD	179.927
152	THR	HG1	5.736
155	GLN	CD	179.93
156	GLN	CD	179.137
169	GLN	CD	179.858
171	ASN	CG	176.443

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1202	857	71.3
¹³C chemical shifts	906	704	77.7
¹⁵N chemical shifts	218	188	86.2

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	398	358	89.9
¹³C chemical shifts	388	346	89.2
¹⁵N chemical shifts	191	172	90.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	804	499	62.1
¹³C chemical shifts	518	358	69.1
¹⁵N chemical shifts	27	16	59.3

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	117	106	90.6
¹³C chemical shifts	117	108	92.3

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	59	55.1
¹³C chemical shifts	106	26	24.5
¹⁵N chemical shifts	1	1	100.0

Redox state of CYS
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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 194, Sequence coverage: 92.8%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 4106
- Weight of restraints: 1.0 (4106)
- Potential type of restraints: square-well-parabolic (4106)
- Range of distance target values: 2.23, 4.52 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 194, Sequence coverage: 75.3%
- Total number of restraints: 265
- Total number of restraints per polymer type: 265
- Weight of restraints: 1.0 (265)
- Potential type of restraints: square-well-parabolic (265)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords H-NOX, cinaciguat, lyase, soluble guanylate cyclase

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Found 1 Document (2.514 seconds)

BMRB: 34077

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Guanylate cyclase soluble subunit beta-1 (E.C.4.6.1.2), entity 1, : 1 : 12 : 52 entities Detail

Interaction partners 1. Guanylate cyclase soluble subunit beta-1 (E.C.4.6.1.2), entity 1, : 4 interactors Detail

Experiments performed 17 experiments Detail

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NMR combined restraints 6 contents Detail