SMTL ID : 1lk6.1

Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

1 x ACE- SER- GLU- ALA- ALA- ALA- SER: antithrombin P14-P9 peptide(Non-covalent)

ACE-SER-GLU-ALA-ALA-ALA-SER.1: 31 residues within 4Å: Chain B: F.77, S.79, V.190, T.194, R.197, I.198, V.201, V.216, N.217, T.218, I.219, Y.220, F.221, K.222, G.223, W.225, F.274, M.281, F.368, H.369, K.370, A.371, F.372, L.373, E.374, V.375, N.376, G.379, I.412, F.422 Ligands: GOL.11 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:F.77, B:I.198, B:Y.220, B:Y.220, B:A.371, B:L.373, B:I.412, B:F.422, B:F.422 Hydrogen bonds: B:I.219, B:I.219, B:F.221, B:F.221, B:G.223, B:G.223, B:K.370, 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, B:H.369

1 x FME- LEU- PHE: exogenous tripeptide formyl-MLF(Non-covalent)

FME-LEU-PHE.2: 17 residues within 4Å: Chain B: F.87, T.90, A.206, T.211, V.212, L.213, V.214, L.215, L.351, L.362, Y.363, V.364, S.365, D.366, A.367, F.368 Ligands: GOL.11 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.90, B:A.206, B:L.213, B:L.213, B:V.214, B:L.351, B:L.362, B:V.364, B:D.366, B:F.368 Hydrogen bonds: B:V.212, B:L.213, B:L.213, B:L.215, B:L.215, B:S.365, B:D.366, B:D.366, B:F.368

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

NDG.3: 2 residues within 4Å: Chain A: C.21, N.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.96, A:N.96 NDG.4: 6 residues within 4Å: Chain A: N.18, 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:N.18, A:N.155, A:T.157 NDG.5: 2 residues within 4Å: Chain A: N.18 Ligands: NDG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.18, A:M.20 NDG.6: 1 residues within 4Å: Chain B: N.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.96 NDG.8: 2 residues within 4Å: Chain B: N.18 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.18 NDG.10: 1 residues within 4Å: Ligands: NAG.9 No protein-ligand interaction detected (PLIP)

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

NAG.7: 5 residues within 4Å: Chain B: N.18, M.20, N.155, A.356 Ligands: NDG.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.356 Hydrogen bonds: B:N.18, B:N.155, B:E.357 NAG.9: 3 residues within 4Å: Chain B: N.192, E.195 Ligands: NDG.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.192, B:E.195

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 9 residues within 4Å: Chain B: S.82, A.86, V.216, N.217, L.331, F.368, H.369 Ligands: ACE-SER-GLU-ALA-ALA-ALA-SER.1, FME-LEU-PHE.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.82, B:S.82, B:N.217, B:F.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, A. et al., Serpin Polymerization Is Prevented by a Hydrogen Bond Network That Is Centered on His-334 and Stabilized by Glycerol. J.Biol.Chem. (2003)

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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