- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x MNA: 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid(Non-covalent)
- 4 x IMD: IMIDAZOLE(Non-covalent)
IMD.2: 4 residues within 4Å:- Chain A: Y.127
- Chain B: Y.263, S.264, Q.265
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- pi-Stacking: A:Y.127
- Hydrogen bonds: B:S.264
IMD.9: 4 residues within 4Å:- Chain C: Y.127
- Chain D: Y.263, S.264, Q.265
1 PLIP interactions:1 interactions with chain C- pi-Stacking: C:Y.127
IMD.13: 4 residues within 4Å:- Chain D: Y.127
- Chain E: Y.263, S.264, Q.265
1 PLIP interactions:1 interactions with chain D- pi-Stacking: D:Y.127
IMD.17: 4 residues within 4Å:- Chain A: Y.263, S.264, Q.265
- Chain E: Y.127
2 PLIP interactions:1 interactions with chain E, 1 interactions with chain A- pi-Stacking: E:Y.127
- Hydrogen bonds: A:S.264
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 6 residues within 4Å:- Chain A: M.85, L.86, N.87, M.90, G.245, D.246
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:L.86, A:N.87, A:N.87
- Water bridges: A:G.245, A:D.246, A:D.246
EDO.4: 5 residues within 4Å:- Chain A: H.139, F.141, F.210, T.212, R.274
2 PLIP interactions:2 interactions with chain A- Water bridges: A:R.274, A:R.274
EDO.5: 3 residues within 4Å:- Chain A: G.125, G.126, Y.127
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:G.125
EDO.7: 3 residues within 4Å:- Chain B: G.125, G.126, Y.127
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:G.125
EDO.10: 6 residues within 4Å:- Chain C: M.85, L.86, N.87, M.90, G.245, D.246
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:L.86, C:N.87, C:N.87
- Water bridges: C:G.245, C:D.246, C:D.246
EDO.11: 2 residues within 4Å:- Chain C: G.126, Y.127
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:G.125
EDO.14: 2 residues within 4Å:- Chain D: G.126, Y.127
1 PLIP interactions:1 interactions with chain D- Water bridges: D:G.125
EDO.15: 4 residues within 4Å:- Chain D: G.28, V.29, R.30, L.284
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:R.30, D:R.30
- Water bridges: D:T.31
EDO.18: 7 residues within 4Å:- Chain E: M.85, L.86, N.87, M.90, G.245, D.246
- Ligands: EDO.22
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:L.86, E:N.87, E:N.87
- Water bridges: E:G.245, E:D.246
EDO.19: 4 residues within 4Å:- Chain E: G.28, V.29, R.30, L.284
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:R.30, E:R.30
EDO.20: 4 residues within 4Å:- Chain E: R.30, T.92, E.94, L.284
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:R.30, E:R.30, E:T.92
- Water bridges: E:E.94, E:E.94
EDO.21: 2 residues within 4Å:- Chain E: G.126, Y.127
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:G.125
EDO.22: 8 residues within 4Å:- Chain E: N.87, L.96, M.97, C.243, K.244, G.245, D.246
- Ligands: EDO.18
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:N.87, E:G.245, E:D.246, E:D.246
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Stroh, L.J. et al., Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family. Mbio (2020)
- Release Date
- 2020-07-08
- Peptides
- Capsid protein VP1: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AAAB
BBBC
CCCD
DDDE
EEE
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x MNA: 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid(Non-covalent)
- 4 x IMD: IMIDAZOLE(Non-covalent)
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Stroh, L.J. et al., Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family. Mbio (2020)
- Release Date
- 2020-07-08
- Peptides
- Capsid protein VP1: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AAAB
BBBC
CCCD
DDDE
EEE