SMTL ID : 4dy7.1 (1 other biounit)

Crystal structures of protease nexin-1 in complex with S195A thrombin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 9 residues within 4Å: Chain A: S.44, Y.45, I.46, D.47, G.48, R.49 Chain B: G.133, Y.134 Ligands: CA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.47, A:G.48, A:R.49 ACT.3: 3 residues within 4Å: Chain B: I.167, V.168, F.186 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.170 ACT.5: 4 residues within 4Å: Chain C: N.221, W.351, F.352, I.353 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.221, C:W.351, C:I.353

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: S.44, D.47, R.49 Chain B: G.133 Ligands: ACT.1 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: A:S.44, A:D.47, A:R.49, B:G.133, ACT.1

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

NA.4: 3 residues within 4Å: Chain B: D.232, R.233, K.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Crystal structures of protease nexin-1 in complex with heparin and thrombin suggest a 2-step recognition mechanism. Blood (2012)

Release Date

2012-08-15

Peptides

Thrombin light chain: A
Thrombin heavy chain: B
Glia-derived nexin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Thrombin light chain

Thrombin heavy chain

Glia-derived nexin

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