SMTL ID : 3pma.3 (3 other biounits)

2.2 Angstrom crystal structure of the complex between Bovine Thrombin and Sucrose Octasulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-4-4-mer

Ligands

4 x GU4- YYJ: 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose(Non-covalent)

GU4-YYJ.1: 12 residues within 4Å: Chain B: D.122, K.123, F.244, K.247, Q.251 Chain D: K.83, Y.85, W.249, K.252, V.253, R.256, L.257 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain B Salt bridges: D:K.83, D:R.256, D:K.252, B:K.123, B:K.247, B:K.247 Hydrogen bonds: D:R.256, D:L.257, B:K.123, B:Q.251, B:Q.251 Water bridges: D:L.257, D:G.258 GU4-YYJ.2: 9 residues within 4Å: Chain B: K.252 Chain D: H.87, P.88, R.98, R.245, L.246, K.248, W.249, K.252 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Water bridges: B:K.252, D:R.89 Salt bridges: B:K.252, D:H.87, D:H.87, D:K.248, D:K.252, D:K.252, D:K.248 Hydrogen bonds: D:K.248, D:W.249, D:R.98 GU4-YYJ.7: 12 residues within 4Å: Chain F: D.122, K.123, F.244, K.247, Q.251 Chain H: K.83, Y.85, W.249, K.252, V.253, R.256, L.257 11 PLIP interactions: 5 interactions with chain H, 6 interactions with chain F Hydrogen bonds: H:Y.85, H:R.256, H:L.257, F:K.123, F:Q.251, F:Q.251 Salt bridges: H:K.83, H:R.256, H:K.252, F:K.123, F:K.247, F:K.247 Water bridges: H:L.257, H:G.258 GU4-YYJ.8: 9 residues within 4Å: Chain F: K.252 Chain H: H.87, P.88, R.98, R.245, L.246, K.248, W.249, K.252 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain F Hydrogen bonds: H:K.248, H:W.249, H:R.98 Salt bridges: H:H.87, H:H.87, H:K.248, H:K.252, H:K.252, F:K.252, H:K.248 Water bridges: F:K.252, H:R.89

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

NA.3: 2 residues within 4Å: Chain B: R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.190, B:K.236 Water bridges: B:D.232 NA.5: 2 residues within 4Å: Chain D: R.233, K.236 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.236 Water bridges: D:G.235, D:G.238 NA.9: 2 residues within 4Å: Chain F: R.233, K.236 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.190, F:K.236 Water bridges: F:D.234 NA.11: 2 residues within 4Å: Chain H: R.233, K.236 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:K.236, H:K.236 Water bridges: H:D.234, H:G.235, H:G.238

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 3 residues within 4Å: Chain F: R.170, P.171 Ligands: CIT.10 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:P.171 Hydrogen bonds: F:R.170 CIT.6: 1 residues within 4Å: Chain D: N.53 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.53, D:N.53 CIT.10: 3 residues within 4Å: Chain B: R.170, P.171 Ligands: CIT.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.171 Hydrogen bonds: B:R.170 CIT.12: 1 residues within 4Å: Chain H: N.53 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:N.53, H:N.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Desai, B.J. et al., Interaction of thrombin with sucrose octasulfate. Biochemistry (2011)

Release Date

2011-07-20

Peptides

Thrombin light chain: ACEG
Thrombin heavy chain: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
A

G
C

B
B

D
D

F
B

H
D

Thrombin light chain

Thrombin heavy chain

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