SMTL ID : 7zn1.1

Avidin + Biotin-Tempo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain C: G.39, N.41, I.58, A.60, L.147 No protein-ligand interaction detected (PLIP)

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

NAG.2: 6 residues within 4Å: Chain A: G.39, N.41, I.58, T.59, A.60, L.147 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.60 Hydrogen bonds: A:G.39, A:N.41 NAG.7: 4 residues within 4Å: Chain B: G.39, N.41, I.58, L.147 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.58 Hydrogen bonds: B:G.39, B:N.41 NAG.14: 4 residues within 4Å: Chain D: G.39, N.41, A.60, L.147 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.60 Hydrogen bonds: D:G.39

4 x KFL: 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide(Non-covalent)

KFL.3: 22 residues within 4Å: Chain A: N.36, L.38, S.40, Y.57, T.59, V.61, T.62, A.63, T.64, W.94, F.96, S.97, S.99, T.101, F.103, W.121, L.123, S.125, R.138, N.142 Chain C: W.134, K.135 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:T.59, A:T.64, A:W.94, A:W.94, A:F.96, A:F.96, A:L.123, A:L.123, C:W.134, C:K.135 Hydrogen bonds: A:N.36, A:S.40, A:T.59, A:T.59, A:A.63, A:T.64, A:S.97, A:S.99, A:S.99, A:N.142, A:N.142 pi-Stacking: A:W.121 KFL.8: 20 residues within 4Å: Chain B: N.36, L.38, S.40, Y.57, T.59, V.61, T.62, W.94, F.96, S.97, S.99, T.101, F.103, W.121, L.123, S.125, R.138, N.142 Chain D: W.134, K.135 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.94, B:F.96, B:F.96, B:L.123 Hydrogen bonds: B:N.36, B:S.40, B:T.59, B:S.97, B:S.99, B:R.138, B:N.142 pi-Stacking: B:W.121 KFL.10: 22 residues within 4Å: Chain A: W.134, K.135 Chain C: N.36, L.38, S.40, Y.57, T.59, V.61, T.62, A.63, T.64, W.94, F.96, S.97, S.99, T.101, F.103, W.121, L.123, S.125, R.138, N.142 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.63, C:W.94, C:W.94, C:F.96, C:F.96, C:L.123 Hydrogen bonds: C:N.36, C:S.40, C:Y.57, C:T.59, C:T.59, C:S.97, C:S.99, C:N.142, C:N.142 KFL.15: 22 residues within 4Å: Chain B: W.134, K.135 Chain D: N.36, L.38, S.40, Y.57, T.59, V.61, T.62, A.63, T.64, W.94, F.96, S.97, S.99, T.101, F.103, W.121, L.123, S.125, R.138, N.142 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:W.94, D:F.96, D:F.96 Hydrogen bonds: D:N.36, D:S.40, D:Y.57, D:T.59, D:T.59, D:T.62, D:A.63, D:T.64, D:S.97, D:S.99, D:S.99, D:S.125, D:S.125, D:N.142 pi-Stacking: D:W.121

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: R.50, E.52 Chain B: P.72, H.74 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.52, B:H.74, H2O.1, H2O.1 ZN.5: 3 residues within 4Å: Chain A: P.72, H.74 Chain B: E.52 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.74, B:E.52, H2O.1, H2O.1 ZN.11: 4 residues within 4Å: Chain C: R.50, E.52 Chain D: P.72, H.74 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:H.74, C:E.52, H2O.2, H2O.2 ZN.12: 3 residues within 4Å: Chain C: P.72, H.74 Chain D: E.52 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:H.74, D:E.52, H2O.2, H2O.2

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain A: D.129, D.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.129, A:D.132 NA.9: 2 residues within 4Å: Chain B: D.129, D.132 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.129 NA.13: 2 residues within 4Å: Chain C: D.129, D.132 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.132 NA.16: 2 residues within 4Å: Chain D: D.129, D.132 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milani, J. et al., Avidin + Biotin-Tempo. To Be Published

Release Date

2023-05-10

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Avidin

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