SMTL ID : 1tb6.1

2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 2 residues within 4Å: Chain B: L.46, N.53 No protein-ligand interaction detected (PLIP)

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-GU4.2: 21 residues within 4Å: Chain B: P.88, R.89, R.98, R.245, K.248, W.249 Chain C: K.11, P.12, R.13, A.43, T.44, N.45, R.46, R.47, V.48, S.112, E.113, K.114, F.122, K.125, R.129 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain C Salt bridges: B:R.89, C:K.11, C:K.125, C:R.46, C:R.47, C:K.114, C:R.47, C:K.114, B:R.245, B:K.248, B:R.89, B:R.89, B:K.248, B:K.248 Hydrogen bonds: C:K.11, C:N.45, C:R.47, C:S.112, C:E.113, C:K.114, B:R.98 Water bridges: B:K.248, B:R.98, B:R.98, B:K.248, B:K.248

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.3: 13 residues within 4Å: Chain C: P.16, M.17, N.18, P.19, M.20, N.155, T.157, Y.158, I.161, P.352, G.353, V.355, E.357 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.157, C:I.161 Hydrogen bonds: C:N.18, C:N.18

1 x NAG- NAG- BMA: 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.4: 1 residues within 4Å: Chain C: N.192 No protein-ligand interaction detected (PLIP)

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 5 residues within 4Å: Chain B: W.148, R.233 Chain C: N.233, R.235, Y.253 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:R.235, B:W.148 MPD.6: 8 residues within 4Å: Chain B: I.9, G.10, S.12, G.64, K.65, H.66, Y.114, L.160 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.9, B:H.66, B:Y.114, B:L.160 Hydrogen bonds: B:G.64, B:K.65 MPD.7: 5 residues within 4Å: Chain B: R.62, K.65, T.69, Y.71, E.76 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.65 MPD.8: 7 residues within 4Å: Chain B: L.130, A.132, V.168, E.169, R.170, F.186, H.242 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.130, B:A.132 Hydrogen bonds: B:R.170, B:R.170 MPD.10: 7 residues within 4Å: Chain C: S.82, N.127, Y.131, L.140, S.142, N.144 Ligands: MPD.12 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:N.127, C:Y.131, C:L.140 Hydrogen bonds: C:S.142, C:N.144 MPD.11: 11 residues within 4Å: Chain C: S.56, A.59, T.60, Y.63, Q.64, E.296, L.299, T.300, P.301, F.411, M.423 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.60, C:Y.63, C:P.301, C:F.411 Hydrogen bonds: C:S.56 MPD.12: 8 residues within 4Å: Chain C: A.124, N.127, Y.131, L.164, V.165, Y.166, G.167 Ligands: MPD.10 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.131 Hydrogen bonds: C:V.165 MPD.13: 5 residues within 4Å: Chain C: P.203, A.206, S.330, D.366, F.368 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.203 Hydrogen bonds: C:S.330

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

NAG.9: 1 residues within 4Å: Chain C: N.96 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin. Nat.Struct.Mol.Biol. (2004)

Release Date

2004-08-17

Peptides

thrombin: A
thrombin: B
Antithrombin-III: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

thrombin

thrombin

Antithrombin-III

Related Entries With Identical Sequence