- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-pentamer
- Ligands
- 4 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)
- 5 x CA: CALCIUM ION(Non-covalent)
CA.5: 2 residues within 4Å:- Chain A: E.23
- Chain B: S.191
5 PLIP interactions:2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: A:E.23, A:E.23, B:S.191, H2O.7, H2O.15
CA.13: 2 residues within 4Å:- Chain B: E.23
- Chain C: S.191
5 PLIP interactions:1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: C:S.191, B:E.23, B:E.23, H2O.27, H2O.28
CA.19: 2 residues within 4Å:- Chain C: E.23
- Chain D: S.191
5 PLIP interactions:1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: C:E.23, D:S.191, H2O.27, H2O.28, H2O.34
CA.22: 2 residues within 4Å:- Chain D: E.23
- Chain E: S.191
4 PLIP interactions:1 interactions with chain E, 2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: E:S.191, D:E.23, D:E.23, H2O.45
CA.26: 3 residues within 4Å:- Chain A: S.191, E.194
- Chain E: E.23
5 PLIP interactions:2 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:E.23, E:E.23, H2O.8, H2O.37, H2O.46
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.6: 7 residues within 4Å:- Chain A: L.167, K.172, D.189, S.191
- Chain E: Y.25, M.97, Y.263
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.172, A:S.191
- Water bridges: A:K.172, A:S.191
EDO.7: 7 residues within 4Å:- Chain A: G.108, G.109, Y.111, Y.251
- Chain B: V.48, A.49, S.50
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:G.109
EDO.8: 7 residues within 4Å:- Chain A: E.194, N.195, R.197, D.224, V.228, G.229, P.230
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:E.194, A:R.197, A:R.197
- Water bridges: A:D.224, A:D.224
EDO.9: 3 residues within 4Å:- Chain A: S.51, A.53
- Ligands: NAG-GAL-SIA.4
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.51, A:S.51
- Water bridges: A:A.53
EDO.10: 6 residues within 4Å:- Chain A: R.197, L.223, D.224
- Chain E: K.93, N.216, S.217
8 PLIP interactions:3 interactions with chain E, 5 interactions with chain A- Hydrogen bonds: E:K.93, A:L.223
- Water bridges: E:K.93, E:N.216, A:R.197, A:R.197, A:R.197, A:E.225
EDO.11: 4 residues within 4Å:- Chain A: V.96, H.128, M.212, Q.213
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:H.128, A:Q.213, A:Q.213
EDO.14: 7 residues within 4Å:- Chain A: Y.25, M.97, Y.263
- Chain B: Q.140, K.172, D.189, S.191
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:K.172, B:S.191
EDO.15: 6 residues within 4Å:- Chain B: Y.25, M.97, Y.263
- Chain C: L.167, K.172, S.191
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:K.172, C:S.191
- Water bridges: C:K.172, C:S.191
EDO.16: 7 residues within 4Å:- Chain A: K.93, N.216, S.217
- Chain B: R.197, L.222, L.223, D.224
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:K.93
- Water bridges: B:V.221
EDO.17: 4 residues within 4Å:- Chain B: F.130, Y.199, T.220
- Ligands: IPA.18
No protein-ligand interaction detected (PLIP)EDO.20: 5 residues within 4Å:- Chain C: L.39, Y.42, H.248, N.250, N.256
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:H.248, C:N.250
- Water bridges: C:N.256
EDO.23: 7 residues within 4Å:- Chain D: G.108, G.109, Y.111, Y.251
- Chain E: A.49, S.50
- Ligands: NAG-GAL-SIA.3
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:G.109, D:G.109
EDO.24: 6 residues within 4Å:- Chain D: E.194, N.195, D.224, V.228, G.229, P.230
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:L.231
EDO.27: 6 residues within 4Å:- Chain D: Y.25, Y.263
- Chain E: Q.140, L.167, K.172, S.191
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:K.172, E:K.172, E:S.191
EDO.28: 3 residues within 4Å:- Chain E: Y.199, T.220
- Ligands: IPA.29
No protein-ligand interaction detected (PLIP)- 5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)
IPA.12: 5 residues within 4Å:- Chain A: H.128, F.130, Y.199, G.200, S.201
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:F.130, A:Y.199
IPA.18: 6 residues within 4Å:- Chain B: H.128, F.130, Y.199, G.200, S.201
- Ligands: EDO.17
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:F.130
IPA.21: 5 residues within 4Å:- Chain C: H.128, F.130, Y.199, G.200, S.201
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:F.130
IPA.25: 6 residues within 4Å:- Chain D: H.128, F.130, Y.199, G.200, S.201, R.262
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:F.130, D:Y.199
IPA.29: 6 residues within 4Å:- Chain E: H.128, F.130, Y.199, G.200, S.201
- Ligands: EDO.28
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:F.130
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Khan, Z.M. et al., Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate. J.Virol. (2014)
- Release Date
- 2014-04-09
- Peptides
- VP1: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-pentamer
- Ligands
- 4 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)
- 5 x CA: CALCIUM ION(Non-covalent)
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Khan, Z.M. et al., Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate. J.Virol. (2014)
- Release Date
- 2014-04-09
- Peptides
- VP1: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E