- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.48 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)
- 5 x CA: CALCIUM ION(Non-covalent)
CA.6: 3 residues within 4Å:- Chain A: E.23
- Chain B: S.191, E.194
5 PLIP interactions:1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: A:E.23, B:S.191, H2O.9, H2O.23, H2O.26
CA.14: 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.34, H2O.34
CA.23: 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.45, H2O.47, H2O.48
CA.29: 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.48, H2O.60
CA.34: 3 residues within 4Å:- Chain A: S.191, E.194
- 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.1, H2O.1, H2O.11
- 5 x CL: CHLORIDE ION(Non-functional Binders)
CL.7: 3 residues within 4Å:- Chain A: I.157, K.158, A.171
Ligand excluded by PLIPCL.15: 4 residues within 4Å:- Chain B: I.157, K.158, K.170, A.171
Ligand excluded by PLIPCL.24: 4 residues within 4Å:- Chain C: I.157, K.158, K.170, A.171
Ligand excluded by PLIPCL.30: 4 residues within 4Å:- Chain D: I.157, K.158, A.171, W.186
Ligand excluded by PLIPCL.35: 4 residues within 4Å:- Chain E: I.157, K.158, K.170, A.171
Ligand excluded by PLIP- 20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.8: 8 residues within 4Å:- Chain A: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267
Ligand excluded by PLIPEDO.9: 5 residues within 4Å:- Chain A: Y.150, P.151, D.152, V.154, A.156
Ligand excluded by PLIPEDO.10: 8 residues within 4Å:- Chain A: E.194, N.195, R.197, D.224, V.228, G.229, P.230, L.231
Ligand excluded by PLIPEDO.11: 4 residues within 4Å:- Chain A: P.73, L.75, W.87, K.270
Ligand excluded by PLIPEDO.12: 4 residues within 4Å:- Chain A: F.130, Y.199, T.220
- Ligands: IPA.13
Ligand excluded by PLIPEDO.16: 8 residues within 4Å:- Chain B: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267
Ligand excluded by PLIPEDO.17: 4 residues within 4Å:- Chain B: N.32, E.37, N.44, D.60
Ligand excluded by PLIPEDO.18: 8 residues within 4Å:- Chain B: E.194, N.195, R.197, D.224, V.228, G.229, P.230, L.231
Ligand excluded by PLIPEDO.19: 4 residues within 4Å:- Chain B: E.8
- Chain C: N.226, G.227, V.228
Ligand excluded by PLIPEDO.20: 6 residues within 4Å:- Chain B: L.74, L.75, N.76, M.79, G.234, D.235
Ligand excluded by PLIPEDO.21: 2 residues within 4Å:- Chain B: N.58, K.59
Ligand excluded by PLIPEDO.25: 8 residues within 4Å:- Chain C: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267
Ligand excluded by PLIPEDO.26: 4 residues within 4Å:- Chain C: N.32, E.37, N.44, D.60
Ligand excluded by PLIPEDO.27: 4 residues within 4Å:- Chain C: L.75, N.76, G.234, D.235
Ligand excluded by PLIPEDO.31: 5 residues within 4Å:- Chain D: L.75, N.76, M.79, G.234, D.235
Ligand excluded by PLIPEDO.32: 5 residues within 4Å:- Chain D: T.94, F.130, Q.213, R.262
- Ligands: IPA.33
Ligand excluded by PLIPEDO.36: 8 residues within 4Å:- Chain E: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267
Ligand excluded by PLIPEDO.37: 2 residues within 4Å:- Chain E: D.152, V.154
Ligand excluded by PLIPEDO.38: 5 residues within 4Å:- Chain E: T.94, F.130, Q.213, R.262
- Ligands: IPA.40
Ligand excluded by PLIPEDO.39: 7 residues within 4Å:- Chain E: E.194, N.195, R.197, D.224, V.228, G.229, L.231
Ligand excluded by PLIP- 5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)
IPA.13: 7 residues within 4Å:- Chain A: H.128, M.129, F.130, Y.199, G.200, S.201
- Ligands: EDO.12
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:F.130
- Hydrogen bonds: A:S.201
- Water bridges: A:R.262
IPA.22: 5 residues within 4Å:- Chain B: H.128, F.130, Y.199, G.200, S.201
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:F.130
- Water bridges: B:S.201, B:S.201, B:R.262
IPA.28: 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.33: 7 residues within 4Å:- Chain D: H.128, M.129, F.130, Y.199, G.200, S.201
- Ligands: EDO.32
1 PLIP interactions:1 interactions with chain D- Hydrophobic interactions: D:F.130
IPA.40: 5 residues within 4Å:- Chain E: H.128, F.130, Y.199, S.201
- Ligands: EDO.38
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:F.130
- Hydrogen bonds: E:H.128
- 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
AB
BC
CD
DE
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.48 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)
- 5 x CA: CALCIUM ION(Non-covalent)
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- 20 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
AB
BC
CD
DE
E