SMTL ID : 1xmn.1 (4 other biounits)

Crystal structure of thrombin bound to heparin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-4-4-mer

Ligands

1 x IDS- SGN- IDS- SGN- IDS- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid(Covalent)

IDS-SGN-IDS-SGN-IDS-SGN.1: 17 residues within 4Å: Chain B: H.87, R.89, R.98, R.123, R.170, F.244, R.245, K.248, W.249 Chain H: H.87, R.89, F.244, R.245, K.248, W.249, K.252 Ligands: GOL.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:R.245, B:R.245 Salt bridges: B:R.123, H:K.252, B:R.170 Water bridges: B:R.170, B:R.170

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.2: 3 residues within 4Å: Chain B: L.46, P.48, N.53 No protein-ligand interaction detected (PLIP)

1 x SGN- IDS- SGN- IDS- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose(Post Translational Modification)

SGN-IDS-SGN-IDS-SGN.3: 16 residues within 4Å: Chain D: H.87, R.89, R.98, R.123, R.245, L.246, K.248, W.249, K.252 Chain F: R.89, R.98, F.244, K.248, W.249, K.252 Ligands: GOL.18 No protein-ligand interaction detected (PLIP)

2 x NAG- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG.4: 3 residues within 4Å: Chain D: L.46, P.48, N.53 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.53 NAG-NDG.5: 2 residues within 4Å: Chain F: L.46, N.53 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.53

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN.6: 3 residues within 4Å: Chain H: L.46, P.48, N.53 No protein-ligand interaction detected (PLIP)

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

0G6.7: 19 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, D.204, S.205, S.226, W.227, G.228, G.230, G.238 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.179, B:W.227 Hydrogen bonds: B:A.200, B:G.203, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230 Water bridges: B:E.202, B:E.202, B:W.227, B:E.229, B:G.230, B:D.232, B:Y.240 Salt bridges: B:D.199 0G6.11: 19 residues within 4Å: Chain D: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, D.204, S.205, S.226, W.227, G.228, G.230, G.238 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.47, D:W.50, D:L.96, D:I.179, D:W.227 Hydrogen bonds: D:A.200, D:G.203, D:S.205, D:S.226, D:G.228, D:G.228, D:G.230 Water bridges: D:W.227, D:E.229, D:G.230, D:G.230, D:Y.240 Salt bridges: D:D.199 0G6.15: 18 residues within 4Å: Chain F: H.43, Y.47, W.50, E.94, L.96, I.179, D.199, A.200, C.201, E.202, G.203, D.204, S.205, S.226, W.227, G.228, G.230, G.238 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:Y.47, F:W.50, F:L.96, F:I.179, F:W.227 Hydrogen bonds: F:A.200, F:G.203, F:S.205, F:S.226, F:G.228, F:G.228, F:G.230 Water bridges: F:W.227, F:E.229, F:G.230, F:G.230, F:Y.240 Salt bridges: F:D.199 0G6.20: 19 residues within 4Å: Chain H: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, D.204, S.205, S.226, W.227, G.228, G.230, G.238 20 PLIP interactions: 20 interactions with chain H Hydrophobic interactions: H:Y.47, H:W.50, H:L.96, H:I.179, H:W.227 Hydrogen bonds: H:A.200, H:G.203, H:S.205, H:S.226, H:G.228, H:G.228, H:G.230 Water bridges: H:E.202, H:E.202, H:W.227, H:E.229, H:G.230, H:G.230, H:Y.240 Salt bridges: H:D.199

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

NA.8: 2 residues within 4Å: Chain B: R.233, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.233, B:K.236 Water bridges: B:R.197, B:R.233 NA.12: 3 residues within 4Å: Chain D: Y.190, R.233, K.236 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.236, D:K.236 Water bridges: D:R.233, D:D.234, D:G.238 NA.16: 3 residues within 4Å: Chain F: Y.190, R.233, K.236 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.190, F:K.236 Water bridges: F:R.233, F:G.235 NA.21: 3 residues within 4Å: Chain H: Y.190, R.233, K.236 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:K.236, H:K.236 Water bridges: H:R.197, H:R.233, H:G.235

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: E.16, S.19, E.21 Chain B: K.212, N.217 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.19, B:K.212, B:K.212, B:N.217 Water bridges: B:N.217 GOL.10: 6 residues within 4Å: Chain B: L.130, I.167, V.168, R.170, F.186 Ligands: IDS-SGN-IDS-SGN-IDS-SGN.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.130, B:R.170, B:R.170 GOL.13: 6 residues within 4Å: Chain C: E.16, S.19, E.21, E.25 Chain D: K.212, N.217 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.19, D:K.212, D:K.212, D:N.217 Water bridges: D:N.217 GOL.14: 3 residues within 4Å: Chain D: E.56, K.83, I.84 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.83 Water bridges: D:F.54, D:K.83 GOL.17: 7 residues within 4Å: Chain E: E.16, S.19, L.20, E.21, E.25 Chain F: K.212, N.217 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:K.212, F:N.217, F:N.217, E:S.19 Water bridges: F:N.217 GOL.18: 5 residues within 4Å: Chain F: L.130, H.242, R.245 Ligands: SGN-IDS-SGN-IDS-SGN.3, GOL.19 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.245, F:R.245 GOL.19: 7 residues within 4Å: Chain F: I.167, V.168, R.170, C.173, F.186, C.187 Ligands: GOL.18 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:V.168, F:R.170, F:R.170, F:C.187, F:C.187 GOL.22: 6 residues within 4Å: Chain G: E.16, S.19, E.21, E.25 Chain H: K.212, N.217 5 PLIP interactions: 1 interactions with chain G, 4 interactions with chain H Hydrogen bonds: G:S.19, H:K.212, H:K.212, H:N.217 Water bridges: H:N.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carter, W.J. et al., Crystal structure of thrombin bound to heparin. J.Biol.Chem. (2005)

Release Date

2004-11-23

Peptides

Thrombin light chain: ACEG
Thrombin heavy chain: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Thrombin light chain

Thrombin heavy chain

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