SMTL ID : 2of8.1

Crystal structure of AVR4 (D39A/C122S)-BNA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 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, A.39, W.68, F.70, S.71, S.73, T.75, W.95, L.97, S.99, R.112, N.116 Chain D: W.108 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:A.39, A:W.68, A:W.68, A:W.68, A:F.70, A:L.97 Hydrogen bonds: A:N.12, A:S.16, A:Y.33, A:T.35, A:A.39, A:S.71, A:S.73, A:S.73, A:R.112, A:N.116 Water bridges: A:N.40 BNI.10: 19 residues within 4Å: Chain B: N.12, L.14, S.16, Y.33, T.35, V.37, A.38, A.39, W.68, F.70, S.71, S.73, T.75, W.95, L.97, S.99, R.112, N.116 Chain C: W.108 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.39, B:W.68, B:W.68, B:W.68, B:F.70 Hydrogen bonds: B:N.12, B:S.16, B:T.35, B:T.35, B:A.39, B:S.71, B:S.73, B:S.73, B:N.116 Water bridges: B:N.40 BNI.14: 19 residues within 4Å: Chain B: W.108 Chain C: N.12, L.14, S.16, Y.33, T.35, V.37, A.38, A.39, W.68, F.70, S.71, S.73, T.75, W.95, L.97, S.99, R.112, N.116 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:A.39, C:W.68, C:W.68, C:W.68, C:F.70, C:L.97 Hydrogen bonds: C:N.12, C:S.16, C:T.35, C:T.35, C:A.39, C:S.71, C:S.73, C:S.73, C:R.112, C:N.116 Water bridges: C:N.40 BNI.23: 19 residues within 4Å: Chain A: W.108 Chain D: N.12, L.14, S.16, Y.33, T.35, V.37, A.38, A.39, W.68, F.70, S.71, S.73, T.75, W.95, L.97, S.99, R.112, N.116 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.39, D:W.68, D:W.68, D:W.68, D:F.70 Hydrogen bonds: D:N.12, D:S.16, D:Y.33, D:T.35, D:A.39, D:S.71, D:S.73, D:S.73, D:N.116 Water bridges: D:N.40

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

FMT.2: 1 residues within 4Å: Chain A: R.26 Ligand excluded by PLIP FMT.3: 3 residues within 4Å: Chain A: L.34, L.46 Ligands: FMT.4 Ligand excluded by PLIP FMT.4: 3 residues within 4Å: Chain A: K.9, I.17 Ligands: FMT.3 Ligand excluded by PLIP FMT.5: 3 residues within 4Å: Chain A: T.11, G.15, I.17 Ligand excluded by PLIP FMT.6: 1 residues within 4Å: Chain A: R.85 Ligand excluded by PLIP FMT.7: 3 residues within 4Å: Chain A: T.45, N.69, F.70 Ligand excluded by PLIP FMT.8: 5 residues within 4Å: Chain A: D.103, I.104 Chain B: Q.59, F.82, I.83 Ligand excluded by PLIP FMT.9: 8 residues within 4Å: Chain A: K.3, C.4, S.5, Q.53, H.54, K.55, A.57, P.60 Ligand excluded by PLIP FMT.11: 2 residues within 4Å: Chain B: Y.106, K.109 Ligand excluded by PLIP FMT.12: 4 residues within 4Å: Chain A: H.67 Chain B: H.54, K.55, R.56 Ligand excluded by PLIP FMT.13: 3 residues within 4Å: Chain A: R.56 Chain B: H.67, N.69 Ligand excluded by PLIP FMT.15: 1 residues within 4Å: Chain C: R.26 Ligand excluded by PLIP FMT.16: 3 residues within 4Å: Chain C: L.34, L.46 Ligands: FMT.17 Ligand excluded by PLIP FMT.17: 3 residues within 4Å: Chain C: K.9, I.17 Ligands: FMT.16 Ligand excluded by PLIP FMT.18: 3 residues within 4Å: Chain C: T.11, G.15, I.17 Ligand excluded by PLIP FMT.19: 1 residues within 4Å: Chain C: R.85 Ligand excluded by PLIP FMT.20: 3 residues within 4Å: Chain C: T.45, N.69, F.70 Ligand excluded by PLIP FMT.21: 5 residues within 4Å: Chain C: D.103, I.104 Chain D: Q.59, F.82, I.83 Ligand excluded by PLIP FMT.22: 8 residues within 4Å: Chain C: K.3, C.4, S.5, Q.53, H.54, K.55, A.57, P.60 Ligand excluded by PLIP FMT.24: 2 residues within 4Å: Chain D: Y.106, K.109 Ligand excluded by PLIP FMT.25: 4 residues within 4Å: Chain C: H.67 Chain D: H.54, K.55, R.56 Ligand excluded by PLIP FMT.26: 3 residues within 4Å: Chain C: R.56 Chain D: H.67, N.69 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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