- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 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.6: 2 residues within 4Å:- Chain A: E.23
- Chain B: S.191
4 PLIP interactions:1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: B:S.191, A:E.23, A:E.23, H2O.14
CA.12: 2 residues within 4Å:- Chain B: E.23
- Chain C: S.191
4 PLIP interactions:2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: B:E.23, B:E.23, C:S.191, H2O.30
CA.16: 3 residues within 4Å:- Chain C: E.23
- Chain D: S.191, E.194
5 PLIP interactions:1 interactions with chain D, 1 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: D:S.191, C:E.23, H2O.25, H2O.31, H2O.38
CA.22: 3 residues within 4Å:- Chain D: E.23
- Chain E: S.191, E.194
5 PLIP interactions:1 interactions with chain E, 2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: E:S.191, D:E.23, D:E.23, H2O.41, H2O.41
CA.28: 2 residues within 4Å:- Chain A: S.191
- Chain E: E.23
5 PLIP interactions:1 interactions with chain A, 1 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: A:S.191, E:E.23, H2O.10, H2O.10, H2O.50
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 5 residues within 4Å:- Chain A: K.172, D.189, S.191
- Chain E: Y.25, M.97
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.8: 7 residues within 4Å:- Chain A: G.108, G.109, Y.111, Y.251
- Chain B: V.48, A.49, S.50
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.109
- Water bridges: A:Y.111
EDO.9: 9 residues within 4Å:- Chain A: E.194, N.195, T.196, R.197, L.222, D.224, V.228, G.229, P.230
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:E.194, A:L.222, A:D.224
- Water bridges: A:R.197, A:L.231, A:L.231
EDO.10: 5 residues within 4Å:- Chain A: K.93, N.216, S.217
- Chain B: R.197, D.224
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Water bridges: B:E.225
- Hydrogen bonds: A:K.93
EDO.13: 4 residues within 4Å:- Chain A: Y.25, Y.263
- Chain B: K.172, S.191
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:K.172, B:K.172, B:S.191
EDO.14: 7 residues within 4Å:- Chain B: G.108, G.109, Y.111, Y.251
- Chain C: V.48, A.49, S.50
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:G.109
- Water bridges: B:Y.111, B:Y.251
EDO.17: 4 residues within 4Å:- Chain B: Y.25, Y.263
- Chain C: K.172, S.191
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:K.172, C:K.172, C:S.191
EDO.18: 5 residues within 4Å:- Chain C: Y.25, M.97
- Chain D: L.167, K.172, S.191
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:K.172, D:S.191
EDO.19: 7 residues within 4Å:- Chain C: G.108, G.109, Y.111, Y.251
- Chain D: V.48, A.49, S.50
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:G.109, C:G.109
- Water bridges: C:Y.111, D:S.50
EDO.20: 5 residues within 4Å:- Chain C: G.31, N.32, N.33, N.34, D.37
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:N.33, C:D.37
- Water bridges: C:G.31, C:N.32
EDO.23: 6 residues within 4Å:- Chain D: Y.25, M.97
- Chain E: Q.140, K.172, D.189, S.191
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:K.172, E:S.191
- Water bridges: E:K.172, E:S.191
EDO.24: 7 residues within 4Å:- Chain D: E.194, N.195, R.197, D.224, V.228, G.229, P.230
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:R.197, D:R.197, D:D.224, D:V.228
EDO.25: 6 residues within 4Å:- Chain D: K.93, N.216, S.217
- Chain E: R.197, L.223, D.224
6 PLIP interactions:3 interactions with chain D, 3 interactions with chain E- Hydrogen bonds: D:K.93, E:L.223
- Water bridges: D:K.93, D:N.216, E:Y.199, E:D.224
EDO.26: 8 residues within 4Å:- Chain C: N.216, S.217
- Chain D: R.197, Y.199, V.221, L.222, L.223, D.224
5 PLIP interactions:4 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:Y.199, D:V.221
- Water bridges: D:R.197, D:E.225, C:K.93
EDO.29: 7 residues within 4Å:- Chain D: G.108, G.109, Y.111, Y.251
- Chain E: V.48, A.49, S.50
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:G.109, D:G.109
- 5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)
IPA.11: 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
- Hydrogen bonds: A:S.201
IPA.15: 5 residues within 4Å:- Chain B: H.128, F.130, Y.199, G.200, S.201
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:F.130, B:Y.199
- Hydrogen bonds: B:H.128
IPA.21: 5 residues within 4Å:- Chain C: H.128, F.130, Y.199, G.200, S.201
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:F.130
- Water bridges: C:H.128
IPA.27: 5 residues within 4Å:- Chain D: H.128, F.130, Y.199, G.200, S.201
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:F.130, D:Y.199
IPA.30: 5 residues within 4Å:- Chain E: H.128, F.130, Y.199, G.200, S.201
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:F.130
- Hydrogen bonds: E:S.201
- 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
FB
GC
HD
IE
J
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 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
FB
GC
HD
IE
J