SMTL ID : 3vhm.1

Crystal structure of NPC-biotin-avidin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NPK: 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid(Non-covalent)

NPK.1: 20 residues within 4Å: Chain A: N.12, D.13, L.14, S.16, Y.33, T.35, V.37, T.38, A.39, T.40, W.70, F.72, S.73, S.75, W.97, L.99, I.117, N.118 Chain C: G.107, W.110 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.14, A:L.14, A:T.35, A:W.70, A:W.70, A:F.72, C:W.110, C:W.110 Hydrogen bonds: A:N.12, A:S.16, A:T.35, A:T.38, A:T.38, A:A.39, A:T.40, A:S.73, A:S.75, A:N.118 NPK.5: 19 residues within 4Å: Chain B: N.12, D.13, L.14, S.16, Y.33, T.35, V.37, T.38, A.39, W.70, F.72, S.73, S.75, W.97, L.99, I.117, N.118, I.119 Chain D: W.110 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:D.13, B:T.35, B:W.70, B:W.70, B:F.72, D:W.110, D:W.110 Hydrogen bonds: B:N.12, B:S.16, B:Y.33, B:T.35, B:T.35, B:T.38, B:A.39, B:T.40, B:S.73, B:S.75, B:N.118 NPK.9: 21 residues within 4Å: Chain A: G.107, W.110 Chain C: N.12, D.13, L.14, S.16, Y.33, T.35, V.37, T.38, A.39, T.40, W.70, S.73, S.75, T.77, F.79, W.97, L.99, I.117, N.118 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.14, C:L.14, C:W.70, C:I.117, A:W.110 Hydrogen bonds: C:N.12, C:S.16, C:T.35, C:T.35, C:T.38, C:T.38, C:A.39, C:T.40, C:S.73, C:S.75, C:N.118 NPK.12: 20 residues within 4Å: Chain B: W.110 Chain D: N.12, D.13, L.14, S.16, Y.33, T.35, V.37, T.38, A.39, T.40, W.70, F.72, S.73, S.75, W.97, L.99, I.117, N.118, I.119 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:D.13, D:W.70, D:W.70, D:F.72, B:W.110, B:W.110 Hydrogen bonds: D:N.12, D:S.16, D:Y.33, D:T.35, D:T.38, D:A.39, D:T.40, D:S.73, D:S.75, D:N.118 Water bridges: D:D.13, D:I.119

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

NAG.2: 6 residues within 4Å: Chain A: K.9, G.15, N.17, I.34, A.36, L.123 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.36 Hydrogen bonds: A:K.9, A:G.15, A:N.17 NAG.6: 6 residues within 4Å: Chain B: G.15, N.17, I.34, T.35, A.36, L.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.15 Water bridges: B:N.17 NAG.10: 3 residues within 4Å: Chain C: G.15, N.17, L.123 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.15, C:N.17 NAG.13: 4 residues within 4Å: Chain D: G.15, N.17, I.34, A.36 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.15, D:N.17 Water bridges: D:K.9

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

SO4.3: 4 residues within 4Å: Chain A: R.2, K.90, E.91, R.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.91 Water bridges: A:K.90 Salt bridges: A:R.2, A:K.90 SO4.4: 2 residues within 4Å: Chain A: R.59, T.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.60, A:T.60 Salt bridges: A:R.59 SO4.7: 2 residues within 4Å: Chain B: K.9, T.19 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.9 SO4.8: 2 residues within 4Å: Chain B: R.59, T.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.60 Salt bridges: B:R.59 SO4.11: 2 residues within 4Å: Chain C: R.59, T.60 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.60, C:T.60 Water bridges: C:Q.61, C:Q.61 Salt bridges: C:R.59 SO4.14: 2 residues within 4Å: Chain D: R.59, T.60 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.60, D:T.60 Water bridges: D:R.59, D:Q.61 Salt bridges: D:R.59

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

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