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SMTL ID : 2afq.1

1.9 angstrom crystal structure of wild-type human thrombin in the sodium free state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-2-2-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1:	4 residues within 4Å: Chain B: H.43, Y.47, L.96 Chain D: R.178 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain B Water bridges: D:R.178, B:H.43, B:Y.47, B:E.202, B:E.202
GOL.2:	6 residues within 4Å: Chain B: R.123, A.126, A.127, H.242, F.244, R.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.242
GOL.3:	6 residues within 4Å: Chain B: M.17, F.19, Q.24, R.62, K.65, R.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.68 Water bridges: B:K.65, B:K.65
GOL.4:	4 residues within 4Å: Chain B: R.178 Chain D: H.43, Y.47, W.50 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Water bridges: D:H.43, D:Y.47, D:E.202, D:E.202, B:R.178
GOL.5:	2 residues within 4Å: Chain D: P.108, A.110 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.35, D:A.110
GOL.6:	1 residues within 4Å: Chain D: D.113 No protein-ligand interaction detected (PLIP)
GOL.7:	8 residues within 4Å: Chain B: D.234 Chain D: L.27, C.28, H.43, K.52, E.202, G.203, S.205 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:H.43, D:K.52, D:E.202, D:G.203, D:S.205, B:D.234, B:D.234

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Johnson, D.J.D. et al., Crystal structure of wild-type human thrombin in the Na+-free state. Biochem.J. (2005)

Release Date

2005-11-15

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

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Prothrombin

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