SMTL ID : 1r1l.1

Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide (formyl-norleucine-LF)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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, E.377, G.379, F.422 Ligands: GOL.10 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:F.77, B:I.198, B:Y.220, B:W.225, B:L.373, 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:E.374, B:N.376 Salt bridges: B:R.197, B:K.222, B:H.369

1 x NLE- LEU- PHE: EXOGENOUS TRIPEPTIDE formyl-(NLE)LF(Non-covalent)

NLE-LEU-PHE.2: 16 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 Ligands: GOL.10, FOR.11 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.87, B:F.87, 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 Hydrogen bonds: B:V.212, B:L.213, B:L.213, B:L.215, B:S.365, B:D.366, B:D.366 Water bridges: B:S.365

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

NAG.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 NAG.4: 6 residues within 4Å: Chain A: N.18, P.19, M.20, N.155, T.157, A.356 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.356 Hydrogen bonds: A:N.18, A:N.18, A:N.155, A:T.157 Water bridges: A:M.20 NAG.5: 2 residues within 4Å: Chain B: C.21, N.96 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.96 Water bridges: B:N.96 NAG.6: 6 residues within 4Å: Chain B: N.18, M.20, N.155, A.356, E.357 Ligands: NAG.7 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.7: 3 residues within 4Å: Chain B: N.18, P.19 Ligands: NAG.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.18 NAG.8: 3 residues within 4Å: Chain B: N.192, E.195 Ligands: NAG.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.192, B:E.195 NAG.9: 1 residues within 4Å: Ligands: NAG.8 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 10 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, NLE-LEU-PHE.2, FOR.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.82, B:N.217, B:N.217

1 x FOR: FORMYL GROUP(Non-covalent)

FOR.11: 6 residues within 4Å: Chain B: L.215, A.367, F.368 Ligands: NLE-LEU-PHE.2, NLE-LEU-PHE.2, GOL.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.368

Links

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Citation

Zhou, A. et al., Serpins and the design of peptides to block intermolecular beta-linkages. To be Published

Release Date

2004-10-05

Peptides

Antithrombin-III: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
I

Antithrombin-III

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