SMTL ID : 1doj.1

Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 1Z0: N-methyl-D-phenylalanyl-N-{(1S)-4-carbamimidamido-1-[(6-carboxy-1,3-benzothiazol-2-yl)carbonyl]butyl}-L-prolinamide(Covalent)

1Z0.1: 21 residues within 4Å: Chain A: H.79, Y.83, W.86, K.88, E.130, N.131, L.132, D.235, A.236, C.237, E.238, G.239, D.240, S.241, V.261, S.262, W.263, G.264, G.266, C.267, G.274 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.83, A:W.86, A:W.86, A:K.88, A:L.132, A:L.132, A:V.261, A:W.263 Hydrogen bonds: A:A.236, A:G.239, A:D.240, A:S.241, A:S.241, A:S.262, A:G.264, A:G.266 Water bridges: A:E.238, A:W.263, A:E.265, A:G.266, A:Y.276 Salt bridges: A:K.88, A:D.235 pi-Stacking: A:W.86

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

NAG.2: 1 residues within 4Å: Chain A: N.89 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.91

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

NA.3: 3 residues within 4Å: Chain A: Y.226, R.269, K.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.272, A:K.272 Water bridges: A:D.270 NA.4: 4 residues within 4Å: Chain A: K.210, T.213, I.215, I.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.213 Water bridges: A:I.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Recacha, R. et al., Structure of human alpha-thrombin complexed with RWJ-51438 at 1.7 A: unusual perturbation of the 60A-60I insertion loop. Acta Crystallogr.,Sect.D (2000)

Release Date

2000-11-03

Peptides

ALPHA-THROMBIN: A
HIRUGEN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ALPHA-THROMBIN

HIRUGEN

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