SMTL ID : 1y55.1

Crystal structure of the C122S mutant of E. Coli expressed avidin related protein 4 (AVR4)-biotin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.00 Å

Oligo State

homo-tetramer

Ligands

4 x BTN: BIOTIN(Non-covalent)

BTN.1: 16 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, N.116 Chain D: W.108 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.68, A:W.68, A:W.68, A:F.70 Hydrogen bonds: A:N.12, A:S.16, A:Y.33, A:T.35, A:D.39, A:S.71, A:S.71, A:S.73, A:N.116 Water bridges: A:N.40 BTN.4: 15 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, T.75, W.95, N.116 Chain C: W.108 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: 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:D.39, B:S.71, B:S.71, B:N.116 Water bridges: B:N.40, B:S.73, B:S.73 BTN.7: 16 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, N.116 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:W.68, C:W.68, C:W.68, C:F.70 Hydrogen bonds: C:N.12, C:S.16, C:T.35, C:T.35, C:D.39, C:S.71, C:S.71, C:S.73, C:N.116 Water bridges: C:D.39, C:N.40 BTN.10: 15 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, T.75, W.95, N.116 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: 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:D.39, D:S.71, D:S.71, D:N.116 Water bridges: D:N.40, D:S.73, D:S.73

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

FMT.2: 5 residues within 4Å: Chain A: A.38, D.39, P.41 Chain D: Y.106, K.109 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.38 FMT.3: 4 residues within 4Å: Chain A: H.54, K.55, R.56 Chain B: H.67 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.55, A:R.56, A:R.56, A:R.56 Water bridges: A:A.57 FMT.5: 4 residues within 4Å: Chain A: H.67 Chain B: H.54, K.55, R.56 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.67, B:K.55, B:R.56 Water bridges: B:A.57 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.8: 5 residues within 4Å: Chain B: Y.106, K.109 Chain C: A.38, D.39, P.41 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.38 FMT.9: 4 residues within 4Å: Chain C: H.54, K.55, R.56 Chain D: H.67 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.55, C:R.56, C:R.56, C:R.56 Water bridges: C:A.57 FMT.11: 4 residues within 4Å: Chain C: H.67 Chain D: H.54, K.55, R.56 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.55, D:R.56, C:H.67 Water bridges: D:A.57 FMT.12: 3 residues within 4Å: Chain D: V.101, N.102, Y.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.102 Water bridges: D:Y.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eisenberg-Domovich, Y. et al., High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-05-24

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

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