SMTL ID : 4mlf.1

Crystal structure for the complex of thrombin mutant D102N and hirudin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1: 3 residues within 4Å: Chain B: D.232, R.233, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:Y.190, B:R.233

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

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

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

ACT.3: 6 residues within 4Å: Chain B: L.130, I.167, V.168, E.169, R.170, F.186 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.167 Water bridges: B:V.168, B:R.170 Salt bridges: B:R.170 ACT.4: 1 residues within 4Å: Chain B: G.4 No protein-ligand interaction detected (PLIP) ACT.5: 5 residues within 4Å: Chain B: D.122, R.123, E.124, F.244, K.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.123 Salt bridges: B:R.123, B:K.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vogt, A.D. et al., Essential role of conformational selection in ligand binding. Biophys.Chem. (2014)

Release Date

2013-09-25

Peptides

Thrombin: A
Thrombin: B
Hirudin variant-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Thrombin

Thrombin

Hirudin variant-1

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