SMTL ID : 1jmo.1

Crystal Structure of the Heparin Cofactor II-S195A Thrombin Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain B: N.54 No protein-ligand interaction detected (PLIP)

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

NA.2: 4 residues within 4Å: Chain B: G.190, Y.191, K.237, Y.238 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.191, B:Y.191 Water bridges: B:G.239

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 8 residues within 4Å: Chain B: L.131, I.168, V.169, R.171, C.174, M.186, F.187, C.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.188 MPD.4: 3 residues within 4Å: Chain B: H.88, W.250, K.253 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.250, B:K.253 MPD.7: 4 residues within 4Å: Chain C: D.124, Q.125, V.126, N.127 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.124 MPD.8: 4 residues within 4Å: Chain C: Q.125, V.126, Y.384, N.385 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.384 Hydrogen bonds: C:Q.125 Water bridges: C:Q.125 MPD.9: 4 residues within 4Å: Chain C: T.177, H.180, K.220, Y.224 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.220, C:Y.224 Hydrogen bonds: C:T.177

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

NAG.5: 3 residues within 4Å: Chain C: V.168, N.169, S.171 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.169, C:S.171 NAG.6: 2 residues within 4Å: Chain C: L.314, N.368 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.368 Hydrogen bonds: C:N.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baglin, T.P. et al., Crystal structures of native and thrombin-complexed heparin cofactor II reveal a multistep allosteric mechanism. Proc.Natl.Acad.Sci.USA (2002)

Release Date

2002-08-30

Peptides

Thrombin, light chain: A
Thrombin, heavy chain: B
HEPARIN COFACTOR II: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
A

Thrombin, light chain

Thrombin, heavy chain

HEPARIN COFACTOR II

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