SMTL ID : 3evj.1

Intermediate structure of antithrombin bound to the natural pentasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 11 residues within 4Å: Chain A: N.18, P.19, M.20, L.92, N.155, T.157, I.161, P.352, G.353, V.355, A.356 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.161 Hydrogen bonds: A:N.18, A:T.157

2 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: 1 residues within 4Å: Chain A: N.192 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: N.18, P.19, M.20, N.155, T.157, A.356 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.18, B:N.18

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

NAG-NAG-MAN-MAN-MAN.4: 2 residues within 4Å: Chain B: K.188, N.192 No protein-ligand interaction detected (PLIP)

2 x ZDO- IDS- SUS- BDP- SGN: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside

ZDO-IDS-SUS-BDP-SGN.5: 13 residues within 4Å: Chain A: K.11, P.12, R.13, A.43, T.44, N.45, R.47, V.48, S.112, E.113, K.114, F.122, R.129 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.45, A:R.46, A:R.47, A:K.114, A:T.44, A:N.45, A:R.13, A:N.45, A:R.47, A:E.113, A:K.114 Salt bridges: A:R.47, A:K.114, A:R.129, A:R.13, A:K.114, A:K.114, A:R.47, A:K.114 ZDO-IDS-SUS-BDP-SGN.6: 16 residues within 4Å: Chain B: K.11, P.12, R.13, E.42, A.43, T.44, N.45, R.47, V.48, S.112, E.113, K.114, Q.118, F.121, F.122, R.129 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.45, B:A.43, B:N.45, B:R.13, B:N.45, B:K.114, B:R.47, B:S.112, B:E.113, B:K.114, B:Q.118 Salt bridges: B:R.47, B:K.114, B:K.114, B:K.114, B:R.47

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

NAG.7: 2 residues within 4Å: Chain A: C.95, N.96 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain B: N.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Langdown, J. et al., The critical role of hinge-region expulsion in the induced-fit heparin binding mechanism of antithrombin. J. Mol. Biol. (2009)

Release Date

2008-10-21

Peptides

Antithrombin-III: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
L

Antithrombin-III

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