SMTL ID : 7sr9.1

Human alpha-thrombin with 180- and 220- loops replaced with homologous loops from protein C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: G.2, S.3, G.4, E.5, A.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.4, A:E.5, A:A.6, A:D.7 SO4.3: 4 residues within 4Å: Chain B: T.147, W.148, T.149, K.154 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.148, B:T.149 Salt bridges: B:K.154 SO4.4: 2 residues within 4Å: Chain B: N.213, R.215 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.213 Salt bridges: B:R.215 SO4.5: 3 residues within 4Å: Chain B: R.170, R.242 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.170, B:R.242 SO4.6: 4 residues within 4Å: Chain B: D.122, R.123, F.241, K.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.123 Salt bridges: B:K.244

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

NAG.2: 2 residues within 4Å: Chain B: L.46, N.53 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.46 Hydrogen bonds: B:N.53

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain B: I.167, V.168, R.170, C.173, F.186, C.187 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.170, B:R.170, B:C.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pelc, L.A. et al., The active site region plays a critical role in Na + binding to thrombin. J.Biol.Chem. (2022)

Release Date

2021-12-08

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

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