- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- homo-pentamer
- Ligands
- 2 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)
- 1 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)
NAG-GAL-SIA.3: 12 residues within 4Å:- Chain A: F.50, S.51, K.52
- Chain E: L.39, Y.42, Q.107, G.108, G.109, H.248, N.250, Y.251, V.256
14 PLIP interactions:13 interactions with chain E, 1 interactions with chain A- Water bridges: E:S.252, E:S.45, E:G.108, E:N.250, E:N.250, E:S.252, A:K.52
- Hydrogen bonds: A:K.52, E:Q.107, E:G.108, E:G.108, E:N.250, E:Y.251
- Hydrophobic interactions: E:L.39, E:Y.42, E:V.256, A:F.50
- 5 x CA: CALCIUM ION(Non-covalent)
CA.4: 3 residues within 4Å:- Chain A: E.23
- Chain B: S.191, E.194
5 PLIP interactions:1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: B:S.191, A:E.23, H2O.5, H2O.19, H2O.19
CA.8: 3 residues within 4Å:- Chain B: E.23
- Chain C: S.191, E.194
5 PLIP interactions:1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: B:E.23, C:S.191, H2O.21, H2O.26, H2O.28
CA.13: 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.28, H2O.37, H2O.38
CA.17: 3 residues within 4Å:- Chain D: E.23
- Chain E: S.191, E.194
5 PLIP interactions:1 interactions with chain E, 1 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: E:S.191, D:E.23, H2O.38, H2O.45, H2O.49
CA.22: 3 residues within 4Å:- Chain A: S.191, E.194
- Chain E: E.23
5 PLIP interactions:2 interactions with chain E, 1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: E:E.23, E:E.23, A:S.191, H2O.5, H2O.47
- 5 x CL: CHLORIDE ION(Non-functional Binders)
CL.5: 3 residues within 4Å:- Chain A: I.157, K.158, A.171
Ligand excluded by PLIPCL.9: 4 residues within 4Å:- Chain B: I.157, K.158, A.171, W.186
Ligand excluded by PLIPCL.14: 4 residues within 4Å:- Chain C: I.157, K.158, K.170, A.171
Ligand excluded by PLIPCL.18: 6 residues within 4Å:- Chain D: I.157, K.158, K.170, A.171, K.172, W.186
Ligand excluded by PLIPCL.23: 3 residues within 4Å:- Chain E: I.157, K.158, A.171
Ligand excluded by PLIP- 9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.6: 7 residues within 4Å:- Chain A: E.194, N.195, R.197, D.224, V.228, G.229, P.230
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.197, A:R.197, A:V.228
- Water bridges: A:N.195
EDO.10: 4 residues within 4Å:- Chain B: T.94, F.130, R.262
- Ligands: IPA.12
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:R.262, B:R.262
- Water bridges: B:V.96, B:Q.213, B:Q.213
EDO.11: 8 residues within 4Å:- Chain B: E.194, N.195, R.197, D.224, V.228, G.229, P.230, L.231
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.197, B:R.197, B:V.228
EDO.15: 4 residues within 4Å:- Chain C: T.94, F.130, R.262
- Ligands: IPA.16
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:Q.213, C:R.262, C:R.262
- Water bridges: C:V.96
EDO.19: 5 residues within 4Å:- Chain D: L.75, N.76, M.79, G.234, D.235
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:L.75, D:N.76, D:N.76, D:N.76
EDO.20: 4 residues within 4Å:- Chain D: T.94, F.130, R.262
- Ligands: IPA.21
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:R.262, D:R.262
- Water bridges: D:V.96, D:Q.213, D:Q.213
EDO.24: 4 residues within 4Å:- Chain E: T.94, Q.213, R.262
- Ligands: IPA.27
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:Q.213, E:R.262, E:R.262
- Water bridges: E:V.96, E:Q.213
EDO.25: 5 residues within 4Å:- Chain E: L.75, N.76, M.79, G.234, D.235
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:L.75, E:N.76, E:N.76, E:N.76
- Water bridges: E:G.234
EDO.26: 7 residues within 4Å:- Chain E: E.194, N.195, R.197, D.224, V.228, G.229, P.230
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:R.197, E:R.197, E:V.228
- Water bridges: E:N.195
- 5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)
IPA.7: 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
- Water bridges: A:R.262
IPA.12: 6 residues within 4Å:- Chain B: H.128, F.130, Y.199, G.200, S.201
- Ligands: EDO.10
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:F.130
IPA.16: 6 residues within 4Å:- Chain C: H.128, F.130, Y.199, G.200, S.201
- Ligands: EDO.15
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:F.130
- Water bridges: C:S.201, C:R.262
IPA.21: 6 residues within 4Å:- Chain D: H.128, F.130, Y.199, G.200, S.201
- Ligands: EDO.20
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:F.130
- Water bridges: D:R.262
IPA.27: 6 residues within 4Å:- Chain E: H.128, F.130, Y.199, G.200, S.201
- Ligands: EDO.24
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:F.130
- Water bridges: E:R.262
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Neu, U. et al., Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands. Plos Pathog. (2013)
- Release Date
- 2013-12-04
- Peptides
- Major Capsid Protein VP1: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
FB
GC
HD
IE
J
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- homo-pentamer
- Ligands
- 2 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)
- 1 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)
- 5 x CA: CALCIUM ION(Non-covalent)
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- 9 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
- Neu, U. et al., Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands. Plos Pathog. (2013)
- Release Date
- 2013-12-04
- Peptides
- Major Capsid Protein VP1: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
FB
GC
HD
IE
J