SMTL ID : 3vxf.1

X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5

Coordinates

PDB Format Compare

Method

NEUTRON DIFFRACTION 2.75 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x DPN- PRO- ARG: BIVALIRUDIN(Non-covalent)

DPN-PRO-ARG.1: 24 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, D.204, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, D.232, G.238, Y.240 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.47, B:L.96, B:L.96, B:W.227 Hydrogen bonds: B:H.43, B:A.200, B:A.200, B:C.201, B:G.203, B:D.204, B:S.205, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230, B:G.230 Water bridges: B:E.229, B:E.229, B:G.230, B:F.239 Salt bridges: B:H.43, B:D.199

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain B: L.46, P.48, N.53, T.55 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.46 Hydrogen bonds: B:N.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamada, T. et al., Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex. Biochim.Biophys.Acta (2013)

Release Date

2013-09-04

Peptides

Thrombin light chain: A
Thrombin heavy chain: B
BIVALIRUDIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
J

Thrombin light chain

Thrombin heavy chain

BIVALIRUDIN

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