SMTL ID : 2b5t.2 (1 other biounit)

2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-1-mer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 1 residues within 4Å: Chain B: N.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.53 NAG-FUC.13: 3 residues within 4Å: Chain D: P.48, N.53, W.92 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.53

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: S.17, G.18, E.19, A.20, D.21 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.17, A:G.18, A:E.19, A:A.20, A:D.21 Water bridges: A:S.17, A:E.19, A:E.19 GOL.3: 3 residues within 4Å: Chain A: D.47 Chain B: Y.134 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.134 GOL.8: 8 residues within 4Å: Chain A: Y.6, Q.7, F.9, E.19 Chain B: L.120, P.121, D.122, K.247 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.6, A:E.19, B:L.120, B:D.122, B:K.247 Water bridges: A:T.8, B:L.120 GOL.9: 8 residues within 4Å: Chain A: T.37, E.40 Chain B: E.3, G.4, S.5, V.162, V.163, N.164 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.4, B:N.164, B:N.164, B:N.164, A:T.37 Water bridges: B:K.196 GOL.10: 9 residues within 4Å: Chain A: Y.45, D.47 Chain B: S.128, L.129, Q.131, Y.134, P.214, F.215 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.131 GOL.11: 5 residues within 4Å: Chain B: F.54, T.55, E.56, K.83, I.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.54, B:K.83, B:K.83 Water bridges: B:I.86 GOL.12: 4 residues within 4Å: Chain B: P.88, W.249, K.252, Q.256 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.86, B:W.249 GOL.18: 6 residues within 4Å: Chain D: P.88, W.249, K.252, Q.256, F.257 Ligands: GU3-GU2-GU6-GU1-GU5-GU8-GU9-GU8-GU9-GU8-GU9-GU8-GU5-GU0-GU6-GU4.14 No protein-ligand interaction detected (PLIP) GOL.19: 7 residues within 4Å: Chain D: L.130, V.168, R.170, C.173, F.186, C.187 Ligands: SO4.17 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.170, D:C.187 Water bridges: D:L.130, D:H.242 GOL.20: 7 residues within 4Å: Chain C: T.37, E.40 Chain D: G.4, S.5, V.162, V.163, N.164 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.37, C:E.40, D:S.5, D:N.164, D:N.164 GOL.21: 5 residues within 4Å: Chain D: R.180, I.181, T.182, D.183 Ligands: GU3-GU2-GU6-GU1-GU5-GU8-GU9-GU8-GU9-GU8-GU9-GU8-GU5-GU0-GU6-GU4.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.180, D:D.183 Water bridges: D:K.174, D:T.182, D:T.182 GOL.24: 5 residues within 4Å: Chain E: R.197, R.324, F.372, E.374, E.381 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.324, E:R.324, E:E.374, E:E.381

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

SO4.4: 2 residues within 4Å: Chain B: R.89, R.98 5 PLIP interactions: 5 interactions with chain B Water bridges: B:D.97, B:R.180, B:N.184 Salt bridges: B:R.89, B:R.98 SO4.5: 2 residues within 4Å: Chain B: R.170 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.170 SO4.6: 6 residues within 4Å: Chain B: L.130, I.167, V.168, R.170, F.186 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain B Water bridges: B:A.132, B:R.170, B:C.187 Salt bridges: B:R.170 SO4.7: 5 residues within 4Å: Chain B: T.69, R.70, S.158 Chain E: A.391, G.392 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:T.69, B:T.69, E:G.392 Salt bridges: B:R.70 SO4.17: 3 residues within 4Å: Chain D: R.170, R.245 Ligands: GOL.19 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.170 Salt bridges: D:R.170, D:R.245 SO4.23: 8 residues within 4Å: Chain B: T.69, R.70, Y.71 Chain E: A.391, G.392, R.393, S.394, L.395 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain E Hydrogen bonds: B:T.69, B:Y.71, E:R.393, E:S.394, E:L.395 Water bridges: E:R.393 Salt bridges: E:R.393

1 x GU3- GU2- GU6- GU1- GU5- GU8- GU9- GU8- GU9- GU8- GU9- GU8- GU5- GU0- GU6- GU4: 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-sulfonato-beta-D-glucopyranose-(1-4)-2,3-di-O-methyl-6-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3-di-O-methyl-6-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-alpha-L-idopyranuronic acid-(1-4)-methyl 3-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranoside(Non-functional Binders)

GU3-GU2-GU6-GU1-GU5-GU8-GU9-GU8-GU9-GU8-GU9-GU8-GU5-GU0-GU6-GU4.14: 28 residues within 4Å: Chain D: H.87, R.89, R.98, R.180, N.184, R.245, L.246, K.248, W.249, K.252 Chain E: C.8, T.9, K.11, P.12, R.13, A.43, T.44, N.45, R.47, V.48, S.112, E.113, K.114, F.122, K.125, R.129 Ligands: GOL.18, GOL.21 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain E Hydrogen bonds: D:R.98, E:K.11, E:N.45, E:R.13, E:R.47, E:K.114, E:R.47, E:S.112, E:E.113, E:K.114, D:K.248, D:W.249, D:R.180, D:R.89, D:N.184 Water bridges: D:N.184, D:N.184, E:R.47, D:N.95, D:D.97 Salt bridges: D:R.89, E:K.11, E:K.125, E:R.47, E:K.114, E:R.47, E:K.114, D:H.87, D:R.89, D:R.89, D:K.248, D:K.248, D:K.252, D:K.252, D:R.98, D:H.87, D:R.89, D:R.98

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

NAG-NAG-BMA-MAN-MAN-MAN-FUC.15: 1 residues within 4Å: Chain E: N.96 No protein-ligand interaction detected (PLIP)

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.16: 1 residues within 4Å: Chain E: N.192 No protein-ligand interaction detected (PLIP)

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

NAG.22: 4 residues within 4Å: Chain E: N.18, M.20, N.155, T.157 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, D.J. et al., Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation. J.Biol.Chem. (2006)

Release Date

2006-09-19

Peptides

Thrombin: AC
Thrombin: BD
Antithrombin-III: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
I

Thrombin

Thrombin

Antithrombin-III

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