SMTL ID : 1z8i.1

Crystal structure of the thrombin mutant G193A bound to PPACK

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 2 residues within 4Å: Chain A: D.13 Chain B: H.116 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.13, B:H.116, H2O.1 ZN.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.5: 2 residues within 4Å: Chain B: H.66, E.72 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.66, B:E.72, H2O.4, H2O.7 ZN.6: 1 residues within 4Å: Chain B: D.6 No protein-ligand interaction detected (PLIP)

1 x 0G6: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide(Covalent)

0G6.2: 20 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, A.203, D.204, S.205, V.225, S.226, W.227, G.228, G.230, G.238 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.50, B:L.96, B:L.96, B:I.179, B:V.225, B:W.227, B:W.227 Hydrogen bonds: B:A.200, B:A.203, B:D.204, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230 Water bridges: B:E.202, B:G.230, B:G.230, B:D.232, B:F.239, B:Y.240 Salt bridges: B:D.199

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

NAG.3: 2 residues within 4Å: Chain B: L.46, N.53 No protein-ligand interaction detected (PLIP)

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

NA.7: 2 residues within 4Å: Chain B: R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:R.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bobofchak, K.M. et al., Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases. J.Biol.Chem. (2005)

Release Date

2005-05-17

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thrombin light chain

Thrombin heavy chain