SMTL ID : 2fhn.1

Avidin related protein AVR4 (C122S, K109I mutant) in complex with BNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 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, R.112, N.116 Chain D: W.108 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:D.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:D.39, A:S.71, A:S.73, A:S.73, A:R.112, A:N.116, A:N.116 Water bridges: A:N.40 BNI.3: 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, R.112, N.116 Chain C: W.108 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:D.39, B:W.68, B:W.68, B:W.68, B:F.70, B:L.97 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.9: 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, R.112, N.116 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:D.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:D.39, C:S.71, C:S.73, C:S.73, C:R.112, C:N.116, C:N.116 Water bridges: C:N.40 BNI.11: 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, R.112, N.116 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:D.39, D:W.68, D:W.68, D:W.68, D:F.70, D:L.97 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

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

FMT.2: 5 residues within 4Å: Chain A: H.54, K.55, R.56 Chain B: H.67 Ligands: FMT.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.55, A:R.56, B:H.67 Water bridges: A:A.57 FMT.4: 3 residues within 4Å: Chain B: H.67, N.69 Ligands: FMT.2 No protein-ligand interaction detected (PLIP) FMT.5: 4 residues within 4Å: Chain A: H.67 Chain B: H.54, K.55, R.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.55, B:R.56 FMT.6: 3 residues within 4Å: Chain B: V.101, N.102, Y.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.102 FMT.7: 5 residues within 4Å: Chain A: Q.59, F.82, I.83 Chain B: D.103, I.104 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.59, A:Q.59, B:I.104 FMT.8: 5 residues within 4Å: Chain B: T.11, N.12, N.13, N.117, T.119 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.119 FMT.10: 5 residues within 4Å: Chain C: H.54, K.55, R.56 Chain D: H.67 Ligands: FMT.12 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.55, C:R.56, D:H.67 Water bridges: C:A.57 FMT.12: 3 residues within 4Å: Chain D: H.67, N.69 Ligands: FMT.10 No protein-ligand interaction detected (PLIP) FMT.13: 4 residues within 4Å: Chain C: H.67 Chain D: H.54, K.55, R.56 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.55, D:R.56 FMT.14: 3 residues within 4Å: Chain D: V.101, N.102, Y.106 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.102 FMT.15: 5 residues within 4Å: Chain C: Q.59, F.82, I.83 Chain D: D.103, I.104 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.59, C:Q.59, D:I.104 FMT.16: 5 residues within 4Å: Chain D: T.11, N.12, N.13, N.117, T.119 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prizant, M. et al., Factors dictating the pseudocatalytic efficiency of avidins. J.Mol.Biol. (2006)

Release Date

2006-03-21

Peptides

Avidin-related protein 4/5: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
Y

C
X

D
Y

Avidin-related protein 4/5