SMTL ID : 1jvq.1

Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive loop peptide, and an exogenous tetrapeptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

1 x ACE- SER- GLU- ALA- ALA- ALA- SER- THR: P14-P8 reactive loop peptide(Non-covalent)

ACE-SER-GLU-ALA-ALA-ALA-SER-THR.1: 34 residues within 4Å: Chain B: F.77, S.79, S.82, I.83, A.86, V.190, T.194, R.197, I.198, V.216, N.217, T.218, I.219, Y.220, F.221, K.222, G.223, W.225, F.274, M.281, L.331, F.368, H.369, K.370, A.371, F.372, L.373, E.374, V.375, N.376, G.379, F.422 Ligands: TRP-MET-ASP-PHE-NH2.2, TRP-MET-ASP-PHE-NH2.2 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:F.77, B:A.86, B:I.198, B:Y.220, B:L.331, B:A.371, B:F.422 Hydrogen bonds: B:S.82, B:S.82, B:N.217, B:N.217, B:I.219, B:I.219, B:F.221, B:F.221, B:G.223, B:G.223, B:F.368, B:K.370, B:K.370, B:F.372, B:F.372, B:E.374, B:E.374, B:N.376 Salt bridges: B:R.197, B:K.222

1 x TRP- MET- ASP- PHE- NH2: exogenous Cholecystokinin tetrapeptide(Non-covalent)

TRP-MET-ASP-PHE-NH2.2: 21 residues within 4Å: Chain B: F.87, T.90, V.201, I.202, A.206, T.211, V.212, L.213, V.214, L.215, V.216, L.351, I.354, L.362, Y.363, V.364, S.365, D.366, A.367, F.368 Ligands: ACE-SER-GLU-ALA-ALA-ALA-SER-THR.1 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:T.90, B:I.202, B:I.202, B:A.206, B:L.213, B:L.213, B:L.215, B:V.216, B:L.351, B:I.354, B:L.362, B:L.362, B:V.364, B:F.368 Hydrogen bonds: B:V.212, B:L.213, B:L.213, B:L.215, B:L.215, B:Y.363, B:S.365, B:S.365, B:D.366, B:D.366, B:F.368

7 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)(Non-functional Binders)

NDG.3: 2 residues within 4Å: Chain A: C.95, N.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.96, A:N.96 NDG.4: 7 residues within 4Å: Chain A: N.18, P.19, M.20, N.155, T.157, A.356 Ligands: NDG.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.356 Hydrogen bonds: A:N.18, A:P.19, A:N.155, A:T.157 NDG.5: 3 residues within 4Å: Chain A: N.18, P.19 Ligands: NDG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.18, A:P.19 NDG.6: 2 residues within 4Å: Chain A: K.188, N.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.192 Salt bridges: A:K.188 NDG.7: 2 residues within 4Å: Chain B: C.95, N.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.96 NDG.9: 3 residues within 4Å: Chain B: N.18, P.19 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.18 NDG.11: 1 residues within 4Å: Ligands: NAG.10 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.8: 8 residues within 4Å: Chain B: N.18, P.19, M.20, N.155, T.157, A.356, E.357 Ligands: NDG.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.356 Hydrogen bonds: B:N.18, B:N.18, B:N.155, B:E.357 NAG.10: 3 residues within 4Å: Chain B: N.192, E.195 Ligands: NDG.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.192, B:E.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, A. et al., How small peptides block and reverse serpin polymerisation. J.Mol.Biol. (2004)

Release Date

2003-06-03

Peptides

ANTITHROMBIN-III: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
I

ANTITHROMBIN-III

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