- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x NAG- GAL- NGC: N-glycolyl-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
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.13, H2O.17
CA.11: 3 residues within 4Å:- Chain B: E.23
- Chain C: S.191, E.194
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.23, H2O.25
CA.18: 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.24, H2O.28, H2O.37
CA.22: 3 residues within 4Å:- Chain D: E.23
- Chain E: S.191, E.194
4 PLIP interactions:2 interactions with chain D, 1 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: D:E.23, D:E.23, E:S.191, H2O.39
CA.26: 2 residues within 4Å:- Chain A: S.191
- Chain E: E.23
5 PLIP interactions:1 interactions with chain E, 1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: E:E.23, A:S.191, H2O.4, H2O.5, H2O.5
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 8 residues within 4Å:- Chain A: E.194, N.195, R.197, D.224, V.228, G.229, P.230, L.231
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.197, A:R.197, A:D.224, A:V.228
EDO.8: 4 residues within 4Å:- Chain A: V.96, H.128, M.212, Q.213
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:H.128, A:Q.213
EDO.9: 6 residues within 4Å:- Chain A: G.108, G.109, Y.111, Y.251
- Chain B: A.49, S.50
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:G.109
EDO.12: 3 residues within 4Å:- Chain B: R.13, T.83, V.272
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.13, B:R.13, B:T.83
EDO.13: 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:2 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:G.109, B:Y.111
- Water bridges: C:S.50
EDO.14: 3 residues within 4Å:- Chain B: Y.111, S.115, Y.251
2 PLIP interactions:2 interactions with chain B- Water bridges: B:S.115, B:S.115
EDO.15: 8 residues within 4Å:- Chain A: Y.25, M.97, Y.263
- Chain B: Q.140, L.167, K.172, D.189, S.191
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:K.172, B:S.191
EDO.16: 4 residues within 4Å:- Chain B: V.96, H.128, M.212, Q.213
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:H.128, B:Q.213
EDO.19: 4 residues within 4Å:- Chain C: V.96, H.128, M.212, Q.213
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:H.128, C:Q.213
- Water bridges: C:Q.213
EDO.20: 4 residues within 4Å:- Chain B: Y.25, Y.263
- Chain C: K.172, S.191
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: C:K.172, C:K.172, C:S.191
- Water bridges: B:E.23
EDO.23: 4 residues within 4Å:- Chain D: V.96, H.128, M.212, Q.213
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:H.128, D:Q.213
EDO.24: 5 residues within 4Å:- Chain D: G.114, S.115, S.116
- Chain E: S.252, E.253
4 PLIP interactions:1 interactions with chain E, 3 interactions with chain D- Hydrogen bonds: E:E.253, D:G.114, D:S.116, D:S.116
EDO.27: 7 residues within 4Å:- Chain D: Y.25, M.97, Y.263
- Chain E: Q.140, K.172, D.189, S.191
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:K.172, E:K.172, E:S.191
EDO.28: 6 residues within 4Å:- Chain E: M.74, L.75, N.76, M.79, G.234, D.235
7 PLIP interactions:7 interactions with chain E- Hydrogen bonds: E:L.75, E:N.76, E:N.76
- Water bridges: E:G.234, E:D.235, E:D.235, E:Y.277
EDO.29: 4 residues within 4Å:- Chain E: V.96, H.128, M.212, Q.213
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:H.128, E:Q.213
- 5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)
IPA.10: 5 residues within 4Å:- Chain A: H.128, F.130, Y.199, S.201, R.262
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:F.130, A:Y.199
- Hydrogen bonds: A:S.201
IPA.17: 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
- Water bridges: 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.25: 4 residues within 4Å:- Chain D: H.128, Y.199, G.200, S.201
No protein-ligand interaction detected (PLIP)IPA.30: 4 residues within 4Å:- Chain E: H.128, F.130, Y.199, S.201
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
FB
GC
HD
IE
J
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x NAG- GAL- NGC: N-glycolyl-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