SMTL ID : 3vhi.1

Crystal structure of monoZ-biotin-avidin complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

4 x VHI: 5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl}pentanoic acid(Non-covalent)

VHI.1: 19 residues within 4Å: Chain A: N.11, D.12, L.13, S.15, Y.32, T.34, V.36, T.37, A.38, T.39, W.69, F.71, S.72, S.74, T.76, W.96, I.116, N.117 Chain C: W.109 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:D.12, A:L.13, A:L.13, A:W.69, A:W.69, A:W.69, A:F.71, C:W.109 Hydrogen bonds: A:S.15, A:Y.32, A:T.34, A:T.34, A:A.38, A:T.39, A:S.72, A:S.72, A:S.74 VHI.5: 21 residues within 4Å: Chain B: N.11, D.12, L.13, S.15, Y.32, T.34, V.36, T.37, A.38, T.39, W.69, F.71, S.72, S.74, T.76, W.96, L.98, I.116, N.117, I.118 Chain D: W.109 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:N.11, B:D.12, B:L.13, B:L.13, B:W.69, B:W.69, B:F.71, B:L.98, B:N.117 Hydrogen bonds: B:N.11, B:S.15, B:T.34, B:T.37, B:A.38, B:T.39, B:S.72, B:S.74 VHI.9: 20 residues within 4Å: Chain A: W.109 Chain C: N.11, D.12, L.13, S.15, Y.32, T.34, V.36, T.37, A.38, T.39, W.69, F.71, S.72, S.74, T.76, W.96, L.98, I.116, N.117 17 PLIP interactions: 1 interactions with chain A, 16 interactions with chain C Hydrophobic interactions: A:W.109, C:D.12, C:L.13, C:L.13, C:T.34, C:W.69, C:W.69, C:W.69, C:F.71 Hydrogen bonds: C:N.11, C:S.15, C:Y.32, C:T.34, C:A.38, C:T.39, C:S.72, C:S.74 VHI.12: 21 residues within 4Å: Chain B: W.109 Chain D: N.11, D.12, L.13, S.15, Y.32, T.34, V.36, T.37, A.38, T.39, W.69, F.71, S.72, S.74, T.76, F.78, W.96, L.98, I.116, N.117 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:D.12, D:L.13, D:L.13, D:W.69, D:W.69, D:F.71, B:W.109 Hydrogen bonds: D:S.15, D:T.34, D:T.34, D:T.37, D:A.38, D:T.39, D:S.72, D:S.74, D:S.74

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

NAG.2: 7 residues within 4Å: Chain A: K.8, G.14, N.16, I.33, T.34, A.35, L.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.8, A:G.14, A:N.16 NAG.6: 5 residues within 4Å: Chain B: G.14, N.16, I.33, T.34, A.35 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.35 Hydrogen bonds: B:G.14 Water bridges: B:N.16 NAG.10: 5 residues within 4Å: Chain C: G.14, N.16, I.33, T.34, A.35 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.35 Hydrogen bonds: C:G.14, C:N.16 NAG.13: 6 residues within 4Å: Chain D: G.14, N.16, I.33, T.34, A.35, L.122 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.35 Hydrogen bonds: D:G.14

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: R.1, K.89, E.90, R.121 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.90 Water bridges: A:K.89, A:E.90 Salt bridges: A:R.1, A:K.89 SO4.4: 2 residues within 4Å: Chain A: R.58, T.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.59 Salt bridges: A:R.58 SO4.7: 2 residues within 4Å: Chain B: K.8, T.18 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.8 Salt bridges: B:K.8 SO4.8: 2 residues within 4Å: Chain B: R.58, T.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.59 Salt bridges: B:R.58 SO4.11: 2 residues within 4Å: Chain C: R.58, T.59 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.59, C:T.59 Salt bridges: C:R.58 SO4.14: 2 residues within 4Å: Chain D: R.58, T.59 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.57, D:T.59 Salt bridges: D:R.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Terai, T. et al., Rational development of caged-biotin protein-labeling agents and some applications in live cells. Chem.Biol. (2011)

Release Date

2011-12-28

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Avidin