SMTL ID : 5afy.1

Thrombin in complex with 3-chloro-benzamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: D.232, R.233, D.234, G.235, K.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.236, A:K.236 Water bridges: A:G.235, A:G.238 NA.2: 4 residues within 4Å: Chain A: K.174, D.175, T.177, R.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.174

1 x WCE: 3-CHLORO-BENZAMIDE(Non-covalent)

WCE.3: 14 residues within 4Å: Chain A: D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238, F.239, Y.240 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.200, A:V.225 Water bridges: A:D.204, A:D.204, A:G.228 Halogen bonds: A:F.239

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 7 residues within 4Å: Chain A: L.130, Q.131, A.132, I.167, V.168, R.170, F.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.170 DMS.5: 4 residues within 4Å: Chain A: E.124, T.125, S.128, F.215 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.128 pi-Cation interactions: A:F.215

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 5 residues within 4Å: Chain A: R.89, N.91, D.97, R.98, R.180 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.91, A:D.97 Water bridges: A:R.89, A:R.89, A:R.89, A:R.180, A:R.180, A:R.180 Salt bridges: A:R.98, A:R.180

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: I.33, S.34, W.37, L.120, I.254 Chain C: E.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.33, A:S.34, A:S.34 GOL.8: 4 residues within 4Å: Chain A: R.170, D.183, H.242, R.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.183, A:D.183 Water bridges: A:R.170, A:H.242

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

NAG.9: 4 residues within 4Å: Chain A: L.46, P.48, N.53, W.92 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.46, A:P.48 Hydrogen bonds: A:N.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruehmann, E. et al., Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why. J.Med.Chem. (2015)

Release Date

2015-08-26

Peptides

Prothrombin: A
Hirudin-2: B
Prothrombin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
L

Prothrombin

Hirudin-2

Prothrombin

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