SMTL ID : 1ypl.1

X-ray crystal structure of thrombin inhibited by synthetic cyanopeptide analogue RA-1008

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-oligomer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain B: R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.238 NA.2: 3 residues within 4Å: Chain B: K.174, D.175, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.177

1 x RA8: N-(BENZYLSULFONYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE(Non-covalent)

RA8.3: 16 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, L.96, I.179, D.199, A.200, S.205, S.226, W.227, G.228, E.229, G.230, C.231, G.238 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:L.96, B:I.179, B:W.227 Hydrogen bonds: B:A.200, B:S.226, B:G.228, B:G.230 Water bridges: B:W.227, B:G.230, B:D.232, B:Y.240 Salt bridges: B:D.199

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain B: P.48, N.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.53 GOL.5: 1 residues within 4Å: Chain B: R.93 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.93, B:R.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Radau, G. et al., Design and X-ray crystal structures of human thrombin with synthetic cyanopeptide-analogues. Pharmazie (2007)

Release Date

2006-01-17

Peptides

thrombin light chain: A
Thrombin heavy chain: B
Hirudin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

thrombin light chain

Thrombin heavy chain

Hirudin

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