SMTL ID : 2ofb.1

Crystal structure of AVR4 (R112L/C122S)-BNA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

homo-tetramer

Ligands

4 x BNI: 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE(Non-covalent)

BNI.1: 19 residues within 4Å: Chain A: N.12, L.14, S.16, Y.33, T.35, V.37, A.38, D.39, W.68, F.70, S.71, S.73, T.75, W.95, L.97, S.99, L.112, N.116 Chain D: W.108 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:D.39, A:W.68, A:W.68, A:W.68, A:F.70, A:L.112, D:W.108 Hydrogen bonds: A:N.12, A:S.16, A:Y.33, A:T.35, A:D.39, A:S.71, A:S.73, A:S.73, A:N.116 Water bridges: A:N.40 BNI.6: 19 residues within 4Å: Chain B: N.12, L.14, S.16, Y.33, T.35, V.37, A.38, D.39, W.68, F.70, S.71, S.73, T.75, W.95, L.97, S.99, L.112, N.116 Chain C: W.108 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:D.39, B:W.68, B:W.68, B:W.68, B:F.70, B:L.97, B:L.112, C:W.108 Hydrogen bonds: B:N.12, B:S.16, B:T.35, B:T.35, B:D.39, B:S.71, B:S.73, B:S.73, B:N.116 Water bridges: B:N.40 BNI.11: 19 residues within 4Å: Chain B: W.108 Chain C: N.12, L.14, S.16, Y.33, T.35, V.37, A.38, D.39, W.68, F.70, S.71, S.73, T.75, W.95, L.97, S.99, L.112, N.116 17 PLIP interactions: 1 interactions with chain B, 16 interactions with chain C Hydrophobic interactions: B:W.108, C:D.39, C:W.68, C:W.68, C:W.68, C:F.70, C:L.112 Hydrogen bonds: C:N.12, C:S.16, C:T.35, C:T.35, C:D.39, C:S.71, C:S.73, C:S.73, C:N.116 Water bridges: C:N.40 BNI.16: 19 residues within 4Å: Chain A: W.108 Chain D: N.12, L.14, S.16, Y.33, T.35, V.37, A.38, D.39, W.68, F.70, S.71, S.73, T.75, W.95, L.97, S.99, L.112, N.116 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:D.39, D:W.68, D:W.68, D:W.68, D:F.70, D:L.97, D:L.112, A:W.108 Hydrogen bonds: D:N.12, D:S.16, D:Y.33, D:T.35, D:D.39, D:S.71, D:S.73, D:S.73, D:N.116 Water bridges: D:N.40

16 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 3 residues within 4Å: Chain A: V.101, N.102, Y.106 Ligand excluded by PLIP FMT.3: 3 residues within 4Å: Chain A: A.36, P.41, I.44 Ligand excluded by PLIP FMT.4: 4 residues within 4Å: Chain A: T.32, L.46, S.47, P.48 Ligand excluded by PLIP FMT.5: 4 residues within 4Å: Chain A: H.54, K.55, R.56 Chain B: H.67 Ligand excluded by PLIP FMT.7: 4 residues within 4Å: Chain A: H.67 Chain B: H.54, K.55, R.56 Ligand excluded by PLIP FMT.8: 4 residues within 4Å: Chain A: K.92 Chain B: D.107, W.108 Chain C: Y.115 Ligand excluded by PLIP FMT.9: 4 residues within 4Å: Chain B: N.13, Y.115, N.117 Ligands: FMT.10 Ligand excluded by PLIP FMT.10: 6 residues within 4Å: Chain B: T.11, N.12, N.13, N.117, T.119 Ligands: FMT.9 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain C: V.101, N.102, Y.106 Ligand excluded by PLIP FMT.13: 3 residues within 4Å: Chain C: A.36, P.41, I.44 Ligand excluded by PLIP FMT.14: 4 residues within 4Å: Chain C: T.32, L.46, S.47, P.48 Ligand excluded by PLIP FMT.15: 4 residues within 4Å: Chain C: H.54, K.55, R.56 Chain D: H.67 Ligand excluded by PLIP FMT.17: 4 residues within 4Å: Chain C: H.67 Chain D: H.54, K.55, R.56 Ligand excluded by PLIP FMT.18: 4 residues within 4Å: Chain A: Y.115 Chain C: K.92 Chain D: D.107, W.108 Ligand excluded by PLIP FMT.19: 4 residues within 4Å: Chain D: N.13, Y.115, N.117 Ligands: FMT.20 Ligand excluded by PLIP FMT.20: 6 residues within 4Å: Chain D: T.11, N.12, N.13, N.117, T.119 Ligands: FMT.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayouka, R. et al., Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester. Acta Crystallogr.,Sect.D (2008)

Release Date

2007-12-25

Peptides

Avidin-related protein 4/5: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Avidin-related protein 4/5

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