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Found 1 Document (0.593 seconds)

BMRB: 16157

2KER

alpha-amylase inhibitor Parvulustat (Z-2685) from Streptomyces parvulus

Authors

Rehm, S., Han, S., Hassani, I., Sokocevic, A., Jonker, H.R.A., Engels, J.W., Schwalbe, H.

Assembly

Parvulustat

Entity

1. Parvulustat (polymer, Thiol state: all disulfide bound), 78 monomers, 8285.937 Da Detail

ATGSPVAECV EYFQSWRYTD VHNGCADAVS VTVEYTHGQW APCRVIEPGG WATFAGYGTD GNYVTGLHTC DPATPSGV

Formula weight

8285.937 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	9:CYS4:SG	1:CYS25:SG
2	disulfide	sing	43:CYS9:SG	1:CYS70:SG

Source organism

Streptomyces parvulus

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 80.9 %, Completeness (bb): 92.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.9 % (660 of 816)	83.3 % (340 of 408)	76.2 % (250 of 328)	87.5 % (70 of 80)
Backbone	92.6 % (424 of 458)	92.5 % (149 of 161)	92.9 % (208 of 224)	91.8 % (67 of 73)
Sidechain	70.9 % (302 of 426)	77.3 % (191 of 247)	62.8 % (108 of 172)	42.9 % (3 of 7)
Aromatic	30.6 % (33 of 108)	57.4 % (31 of 54)	0.0 % (0 of 51)	66.7 % (2 of 3)
Methyl	91.0 % (71 of 78)	92.3 % (36 of 39)	89.7 % (35 of 39)

1. Parvulustat

ATGSPVAECV EYFQSWRYTD VHNGCADAVS VTVEYTHGQW APCRVIEPGG WATFAGYGTD GNYVTGLHTC DPATPSGV

Show sample condition

Sample #1

Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	Parvulustat	[U-100% 13C; U-100% 15N]	0.5 mM
2	sodium phosphate	natural abundance	30 mM
3	sodium chloride	natural abundance	170 mM
4	sodium azide	natural abundance	0.01 %
5	D2O	natural abundance	7.5 %
6	H2O	natural abundance	92.5 %

Sample #2

Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
7	Parvulustat	[U-100% 15N]	0.5 mM
8	sodium phosphate	natural abundance	30 mM
9	sodium chloride	natural abundance	170 mM
10	sodium azide	natural abundance	0.01 %
11	D2O	natural abundance	7.5 %
12	H2O	natural abundance	92.5 %

Sample #3

Solvent system 100% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
13	Parvulustat	[U-100% 13C; U-100% 15N]	0.5 mM
14	sodium phosphate	natural abundance	30 mM
15	sodium chloride	natural abundance	170 mM
16	sodium azide	natural abundance	0.01 %
17	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
18	Parvulustat	[U-100% 15N]	0.5 mM
19	sodium phosphate	natural abundance	30 mM
20	sodium chloride	natural abundance	170 mM
21	sodium azide	natural abundance	0.01 %
22	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	protons	null	indirect	0.2514495
¹H	TSP	protons	external	direct	1.0
¹⁵N	TSP	protons	null	indirect	0.1013291

Referencing offset: 2.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	protons	null	indirect	0.2514495
¹H	TSP	protons	external	direct	1.0
¹⁵N	TSP	protons	null	indirect	0.1013291

Referencing offset: 2.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	protons	null	indirect	0.2514495
¹H	TSP	protons	external	direct	1.0
¹⁵N	TSP	protons	null	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	protons	null	indirect	0.2514495
¹H	TSP	protons	external	direct	1.0
¹⁵N	TSP	protons	null	indirect	0.1013291

Referencing offset: 2.69 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KER, Strand ID: A Detail

Release date

2009-03-29

Citation

The high resolution NMR structure of parvulustat (Z-2685) from Streptomyces parvulus FH-1641: comparison with tendamistat from Streptomyces tendae 4158
Rehm, S., Han, S., Hassani, I., Sokocevic, A., Jonker, H.R.A., Engels, J.W., Schwalbe, H.
Chembiochem. (2009), 10, 119-127, PubMed 19067455 , DOI 10.1002/cbic.200800547 , Abstract

Related entities 1. Parvulustat, : 1 : 1 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
7	Parvulustat	[U-100% 15N]	0.5 mM
8	sodium phosphate	natural abundance	30 mM
9	sodium chloride	natural abundance	170 mM
10	sodium azide	natural abundance	0.01 %
11	D2O	natural abundance	7.5 %
12	H2O	natural abundance	92.5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
13	Parvulustat	[U-100% 13C; U-100% 15N]	0.5 mM
14	sodium phosphate	natural abundance	30 mM
15	sodium chloride	natural abundance	170 mM
16	sodium azide	natural abundance	0.01 %
17	D2O	natural abundance	100 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
7	Parvulustat	[U-100% 15N]	0.5 mM
8	sodium phosphate	natural abundance	30 mM
9	sodium chloride	natural abundance	170 mM
10	sodium azide	natural abundance	0.01 %
11	D2O	natural abundance	7.5 %
12	H2O	natural abundance	92.5 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
18	Parvulustat	[U-100% 15N]	0.5 mM
19	sodium phosphate	natural abundance	30 mM
20	sodium chloride	natural abundance	170 mM
21	sodium azide	natural abundance	0.01 %
22	D2O	natural abundance	100 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
7	Parvulustat	[U-100% 15N]	0.5 mM
8	sodium phosphate	natural abundance	30 mM
9	sodium chloride	natural abundance	170 mM
10	sodium azide	natural abundance	0.01 %
11	D2O	natural abundance	7.5 %
12	H2O	natural abundance	92.5 %

6 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
13	Parvulustat	[U-100% 13C; U-100% 15N]	0.5 mM
14	sodium phosphate	natural abundance	30 mM
15	sodium chloride	natural abundance	170 mM
16	sodium azide	natural abundance	0.01 %
17	D2O	natural abundance	100 %

7 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	Parvulustat	[U-100% 13C; U-100% 15N]	0.5 mM
2	sodium phosphate	natural abundance	30 mM
3	sodium chloride	natural abundance	170 mM
4	sodium azide	natural abundance	0.01 %
5	D2O	natural abundance	7.5 %
6	H2O	natural abundance	92.5 %

8 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	Parvulustat	[U-100% 13C; U-100% 15N]	0.5 mM
2	sodium phosphate	natural abundance	30 mM
3	sodium chloride	natural abundance	170 mM
4	sodium azide	natural abundance	0.01 %
5	D2O	natural abundance	7.5 %
6	H2O	natural abundance	92.5 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	Parvulustat	[U-100% 13C; U-100% 15N]	0.5 mM
2	sodium phosphate	natural abundance	30 mM
3	sodium chloride	natural abundance	170 mM
4	sodium azide	natural abundance	0.01 %
5	D2O	natural abundance	7.5 %
6	H2O	natural abundance	92.5 %

10 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	Parvulustat	[U-100% 13C; U-100% 15N]	0.5 mM
2	sodium phosphate	natural abundance	30 mM
3	sodium chloride	natural abundance	170 mM
4	sodium azide	natural abundance	0.01 %
5	D2O	natural abundance	7.5 %
6	H2O	natural abundance	92.5 %

11 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 92.5% H2O/7.5% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
7	Parvulustat	[U-100% 15N]	0.5 mM
8	sodium phosphate	natural abundance	30 mM
9	sodium chloride	natural abundance	170 mM
10	sodium azide	natural abundance	0.01 %
11	D2O	natural abundance	7.5 %
12	H2O	natural abundance	92.5 %

12 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 318 K, pH 6.6

#	Name	Isotope labeling	Concentration
13	Parvulustat	[U-100% 13C; U-100% 15N]	0.5 mM
14	sodium phosphate	natural abundance	30 mM
15	sodium chloride	natural abundance	170 mM
16	sodium azide	natural abundance	0.01 %
17	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16157_2ker.nef
Input source #2: Coordindates	2ker.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:9:CYS:SG	A:25:CYS:SG	oxidized, CA 51.85, CB 38.617 ppm	oxidized, CA 50.79, CB 39.528 ppm	2.032
A:43:CYS:SG	A:70:CYS:SG	oxidized, CA 53.574, CB 39.464 ppm	oxidized, CA 51.95, CB 43.32 ppm	2.031

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

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------
ATGSPVAECVEYFQSWRYTDVHNGCADAVSVTVEYTHGQWAPCRVIEPGGWATFAGYGTDGNYVTGLHTCDPATPSGV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ATGSPVAECVEYFQSWRYTDVHNGCADAVSVTVEYTHGQWAPCRVIEPGGWATFAGYGTDGNYVTGLHTCDPATPSGV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	78	0	0	100.0

Content subtype: combined_16157_2ker.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	692		96.2 (chain: A, length: 78)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1928 (1)	noe	88.5 (chain: A, length: 78)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	38 (1)	hbond	28.2 (chain: A, length: 78)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	64 (64)	.	56.4 (chain: A, length: 78)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	54 (54)	.	69.2 (chain: A, length: 78)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 96.2%
- Total number of assignments
  - ¹H chemical shifts: 372
  - ¹³C chemical shifts: 250
  - ¹⁵N chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	408	340	83.3
¹³C chemical shifts	328	250	76.2
¹⁵N chemical shifts	82	70	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	149	92.5
¹³C chemical shifts	156	142	91.0
¹⁵N chemical shifts	73	67	91.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	247	191	77.3
¹³C chemical shifts	172	108	62.8
¹⁵N chemical shifts	9	3	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	36	92.3
¹³C chemical shifts	39	35	89.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	31	57.4
¹³C chemical shifts	51	0	0.0
¹⁵N chemical shifts	3	2	66.7

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 88.5%
- Total number of restraints: 1917
- Weight of restraints: 1.0 (1917)
- Potential type of restraints: square-well-parabolic (1917)
- Range of distance target values: 1.72, 4.89 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 28.2%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 56.4%
- Total number of restraints: 64
- Total number of restraints per polymer type: 64
- Weight of restraints: 1.0 (64)
- Potential type of restraints: square-well-parabolic (64)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 69.2%

--------10--------20--------30--------40--------50--------60--------70--------
ATGSPVAECVEYFQSWRYTDVHNGCADAVSVTVEYTHGQWAPCRVIEPGGWATFAGYGTDGNYVTGLHTCDPATPSGV
      ||||||| |  ||||||   |||||||||||| || ||||| |||| ||||| ||||||||||||       
......AECVEYF.S..YTDVHN...DAVSVTVEYTHG.WA.CRVIE.GGWA.FAGYG.DGNYVTGLHTCD       
--------10--------20--------30--------40--------50--------60--------70-

Total number of restraints: 54
Potential type of restraints: undefined (54)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords alpha-amylase inhibitor, Parvulustat (Z-2685)

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Found 1 Document (0.593 seconds)

BMRB: 16157

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Parvulustat, : 1 : 1 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail