SMTL ID : 6px5.1

CRYSTAL STRUCTURE OF HUMAN MEIZOTHROMBIN DESF1 MUTANT S195A bound with PPACK

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-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: 2 residues within 4Å: Chain A: K.68 Chain B: N.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.68

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: E.58, V.84, E.86 Chain B: D.183 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.183, A:E.58, A:E.86, H2O.1, H2O.1 ZN.3: 2 residues within 4Å: Chain A: H.19 Chain B: E.94 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.94, B:E.94, A:H.19, H2O.2

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

0G6.4: 17 residues within 4Å: Chain B: C.28, H.43, Y.47, W.50, E.94, L.96, I.179, D.199, A.200, E.202, G.203, V.225, S.226, W.227, G.228, G.230, G.238 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:H.43, B:Y.47, B:L.96, B:I.179, B:E.202, B:V.225, B:W.227 Hydrogen bonds: B:G.203, B:S.226, B:G.228, B:G.228, B:G.230 Water bridges: B:W.227, B:D.232, B:Y.240 Salt bridges: B:D.199, B:E.202

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

NA.5: 3 residues within 4Å: Chain B: Y.190, R.233, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235, B:G.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pelc, L.A. et al., Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Sci Rep (2019)

Release Date

2019-09-04

Peptides

Prothrombin: A
Prothrombin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
B

Prothrombin

Prothrombin

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