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SMTL ID : 1rd3.1 (2 other biounits)

2.5A Structure of Anticoagulant Thrombin Variant E217K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NDG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NDG-BMA-MAN-FUC.1:

2 residues within 4Å:

Chain B: P.48, N.53

2 PLIP interactions:

2 interactions with chain B

Hydrophobic interactions: B:P.48
Hydrogen bonds: B:N.53

1 x NAG- NDG- FUC: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NDG-FUC.2:

3 residues within 4Å:

Chain D: L.46, P.48, N.53

1 PLIP interactions:

1 interactions with chain D

Hydrogen bonds: D:N.53

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3:	4 residues within 4Å: Chain B: L.130, V.168, R.170, F.186 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.130, B:A.132, B:R.170 Water bridges: B:C.187
PO4.4:	1 residues within 4Å: Chain B: R.73 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.73, B:R.73 Salt bridges: B:R.73
PO4.10:	5 residues within 4Å: Chain D: L.130, I.167, V.168, R.170, F.186 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.130, D:R.170 Water bridges: D:V.168 Salt bridges: D:R.170

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:	5 residues within 4Å: Chain A: E.16, S.19, E.25 Chain B: K.212, N.217 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.212, B:N.217, A:S.19
GOL.6:	5 residues within 4Å: Chain B: D.6, L.144, P.157, S.158, V.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.158 Water bridges: B:Q.161
GOL.7:	10 residues within 4Å: Chain B: E.8, I.9, G.10, M.11, S.12, P.13, G.64, K.65, H.66, Y.114 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.10, B:M.11, B:S.12, B:H.66, B:Y.114
GOL.8:	8 residues within 4Å: Chain B: Y.47, W.92, R.93, E.94, L.96, W.227 Chain D: W.148, R.233 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Y.47, B:W.92, B:E.94, D:R.233, D:R.233
GOL.9:	6 residues within 4Å: Chain B: R.36, E.82, K.104, F.257, G.258, E.259 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.36, B:K.104, B:K.104, B:G.258, B:E.259
GOL.11:	6 residues within 4Å: Chain C: E.16, S.19, L.20, E.21 Chain D: K.212, N.217 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.212, D:N.217, C:S.19

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Carter, W.J. et al., Crystal Structure of Anticoagulant Thrombin Variant E217K Provides Insights into Thrombin Allostery. J.Biol.Chem. (2004)

Release Date

2004-05-04

Peptides

Prothrombin: AC
Prothrombin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Prothrombin

Prothrombin

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