SMTL ID : 4rko.1

Crystal structure of thrombin mutant S195T bound with PPACK

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-mer

Ligands

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

0G6.1: 19 residues within 4Å: Chain A: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, T.205, V.225, S.226, W.227, G.228, G.230, G.238 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.47, A:L.96, A:L.96, A:I.179, A:T.205, A:V.225, A:W.227 Hydrogen bonds: A:A.200, A:G.203, A:T.205, A:S.226, A:G.228, A:G.228, A:G.230 Water bridges: A:W.227, A:Y.240 Salt bridges: A:D.199

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 6 residues within 4Å: Chain A: H.87, R.89, R.245, L.246, K.248, W.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.249 Water bridges: A:K.248 Salt bridges: A:H.87

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: K.212, N.217 Chain B: E.22, S.25, L.26, E.27, E.31 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.212, A:N.217, A:N.217, B:E.31 GOL.4: 5 residues within 4Å: Chain A: L.130, I.167, V.168, R.170, F.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.132, A:V.168, A:R.170 Water bridges: A:R.170

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

NA.5: 2 residues within 4Å: Chain A: R.233, K.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.233, A:K.236 Water bridges: A:G.235, A:G.238

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

NAG.6: 1 residues within 4Å: Chain A: N.53 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pelc, L.A. et al., Why ser and not thr brokers catalysis in the trypsin fold. Biochemistry (2015)

Release Date

2015-03-11

Peptides

Thrombin heavy chain: A
Thrombin light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Thrombin heavy chain

Thrombin light chain

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