SMTL ID : 5chk.1

Crystal structure of avidin - HABA complex (hexagonal crystal form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: G.15, N.17, T.34, T.35, L.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.15, A:N.17 NAG.3: 5 residues within 4Å: Chain B: G.15, N.17, T.34, T.35, L.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.15, B:N.17 NAG.5: 5 residues within 4Å: Chain C: G.15, N.17, T.34, T.35, L.123 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.15, C:N.17 NAG.7: 5 residues within 4Å: Chain D: G.15, N.17, T.34, T.35, L.123 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.15, D:N.17

4 x 55R: 2-[2-(4-oxocyclohexa-2,5-dien-1-ylidene)hydrazinyl]benzoic acid(Non-covalent)

55R.2: 14 residues within 4Å: Chain A: N.12, S.16, Y.33, T.35, V.37, T.38, W.70, S.73, T.77, F.79, W.97, L.99, N.118 Chain B: W.110 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.37, A:T.38, A:T.77, A:F.79, A:L.99, B:W.110 Hydrogen bonds: A:N.12, A:S.16, A:T.35, A:S.73, A:T.77 Water bridges: A:S.75 pi-Stacking: A:W.70, A:W.70, A:W.97, A:W.97 55R.4: 14 residues within 4Å: Chain A: W.110 Chain B: N.12, S.16, Y.33, T.35, V.37, T.38, W.70, S.73, T.77, F.79, W.97, L.99, N.118 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.37, B:T.38, B:T.77, B:F.79, B:L.99, A:W.110 Hydrogen bonds: B:N.12, B:S.16, B:T.35, B:S.73, B:T.77 Water bridges: B:S.75 pi-Stacking: B:W.70, B:W.70, B:W.97, B:W.97 55R.6: 14 residues within 4Å: Chain C: N.12, S.16, Y.33, T.35, V.37, T.38, W.70, S.73, T.77, F.79, W.97, L.99, N.118 Chain D: W.110 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.37, C:T.38, C:T.77, C:F.79, C:L.99, D:W.110 Hydrogen bonds: C:N.12, C:S.16, C:Y.33, C:S.73 Water bridges: C:S.75 pi-Stacking: C:W.70, C:W.70, C:W.97, C:W.97 55R.8: 14 residues within 4Å: Chain C: W.110 Chain D: N.12, S.16, Y.33, T.35, V.37, T.38, W.70, S.73, T.77, F.79, W.97, L.99, N.118 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.37, D:T.38, D:T.77, D:F.79, D:L.99, C:W.110 Hydrogen bonds: D:N.12, D:S.16, D:Y.33, D:S.73 Water bridges: D:S.75 pi-Stacking: D:W.70, D:W.70, D:W.97, D:W.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strzelczyk, P. et al., Crystal structure and ligand affinity of avidin in the complex with 4-hydroxyazobenzene-2-carboxylic acid. J.Mol.Struct. (2016)

Release Date

2016-03-23

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Avidin

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