- 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)
- 3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 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 B, 1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: B:E.52, A:H.74, 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 D, 1 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: D:E.52, C:H.74, 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.132
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.132
- 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
AB
BC
CD
D
- 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)
- 3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 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)
- 4 x ZN: ZINC ION(Non-covalent)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 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
AB
BC
CD
D