SMTL ID : 1vyo.1

Crystal structure of avidin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: L.14, Y.33, T.35, V.37, W.70, T.77, W.97, L.99, N.118 Chain C: W.110 Ligands: GOL.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.33, A:T.35, A:T.35, A:T.77, A:N.118, A:N.118 Water bridges: A:N.12 GOL.2: 11 residues within 4Å: Chain A: V.37, T.38, A.39, T.40, W.70, F.72, S.73, S.75, L.99 Chain C: W.110 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.39, A:S.73, A:S.73, A:S.75 GOL.3: 6 residues within 4Å: Chain A: L.14, G.116, I.117 Chain B: K.94 Chain C: D.109, W.110 7 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:D.109, C:D.109, A:I.117, B:K.94 Water bridges: C:D.109, C:W.110, A:V.115 GOL.4: 5 residues within 4Å: Chain A: A.22, N.24, E.28, F.29, T.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.24, A:N.24, A:T.30 GOL.5: 11 residues within 4Å: Chain B: L.14, Y.33, T.35, V.37, W.70, T.77, W.97, L.99, N.118 Chain D: W.110 Ligands: GOL.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.35, B:T.77, B:T.77, B:N.118, B:N.118 Water bridges: B:N.12, B:T.35 GOL.6: 10 residues within 4Å: Chain B: V.37, T.38, A.39, W.70, F.72, S.73, S.75, L.99 Chain D: W.110 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.38, B:A.39, B:S.73, B:S.73, B:S.75 GOL.7: 11 residues within 4Å: Chain A: W.110 Chain C: L.14, Y.33, T.35, V.37, W.70, T.77, W.97, L.99, N.118 Ligands: GOL.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.33, C:T.35, C:T.35, C:T.77, C:N.118, C:N.118 Water bridges: C:N.12 GOL.8: 11 residues within 4Å: Chain A: W.110 Chain C: V.37, T.38, A.39, T.40, W.70, F.72, S.73, S.75, L.99 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.39, C:S.73, C:S.73, C:S.75 GOL.9: 6 residues within 4Å: Chain A: D.109, W.110 Chain C: L.14, G.116, I.117 Chain D: K.94 7 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:I.117, A:D.109, A:D.109, D:K.94 Water bridges: C:V.115, A:D.109, A:W.110 GOL.10: 5 residues within 4Å: Chain C: A.22, N.24, E.28, F.29, T.30 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.24, C:N.24, C:T.30 GOL.11: 11 residues within 4Å: Chain B: W.110 Chain D: L.14, Y.33, T.35, V.37, W.70, T.77, W.97, L.99, N.118 Ligands: GOL.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.35, D:T.77, D:T.77, D:N.118, D:N.118 Water bridges: D:N.12, D:T.35 GOL.12: 10 residues within 4Å: Chain B: W.110 Chain D: V.37, T.38, A.39, W.70, F.72, S.73, S.75, L.99 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.38, D:A.39, D:S.73, D:S.73, D:S.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Repo, S. et al., Binding Properties of Haba-Type Azo Derivatives to Avidin and Avidin-Related Protein 4. Chem.Biol. (2006)

Release Date

2005-07-20

Peptides

AVIDIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

AVIDIN

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