SMTL ID : 7zyl.1

Avidin + Biotin-Tempo

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 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 A: G.39, N.41, I.58, A.60, L.147 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: G.39, N.41, I.58, A.60, L.147 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain C: G.39, N.41, I.58, A.60, L.147 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain D: G.39, N.41, I.58, A.60, L.147 No protein-ligand interaction detected (PLIP)

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.5: 21 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 D: W.134 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.94, A:W.94, A:F.96, A:F.96, A:L.123 Hydrogen bonds: A:N.36, A:S.40, A:V.61, A:A.63, A:S.97, A:S.99, A:N.142, A:N.142 KFL.6: 21 residues within 4Å: Chain B: 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.94, B:W.94, B:F.96, B:F.96, B:L.123 Hydrogen bonds: B:N.36, B:S.40, B:Y.57, B:T.59, B:V.61, B:S.97, B:S.99, B:N.142, B:N.142 KFL.7: 21 residues within 4Å: Chain B: W.134 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 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.94, C:W.94, C:F.96, C:F.96, C:L.123 Hydrogen bonds: C:N.36, C:S.40, C:V.61, C:S.97, C:S.99, C:N.142, C:N.142 KFL.8: 21 residues within 4Å: Chain A: W.134 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 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.94, D:W.94, D:F.96, D:F.96, D:L.123 Hydrogen bonds: D:N.36, D:S.40, D:Y.57, D:T.59, D:V.61, D:S.97, D:S.99, D:N.142, D:N.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2023-06-14

Peptides

Avidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Avidin

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