- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.48 Å
- Oligo State
- homo-pentamer
- Ligands
- 2 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)
- 2 x BGC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-functional Binders)
BGC-GAL-SIA.3: 12 residues within 4Å:- Chain D: L.39, Y.42, Q.107, G.108, G.109, H.248, N.250, Y.251, V.256
- Chain E: F.50, S.51, K.52
15 PLIP interactions:1 interactions with chain E, 14 interactions with chain D- Hydrogen bonds: E:K.52, D:Q.107, D:G.108, D:G.108, D:N.250, D:Y.251
- Water bridges: E:F.50, E:S.51, E:A.53, D:S.252, D:N.44, D:S.45, D:G.108, D:N.250, D:S.252, D:T.254, E:K.52, E:K.52
- Hydrophobic interactions: D:L.39, D:Y.42, D:V.256
BGC-GAL-SIA.4: 11 residues within 4Å:- Chain A: S.51, K.52
- Chain E: L.39, Y.42, Q.107, G.108, G.109, H.248, N.250, Y.251, V.256
15 PLIP interactions:13 interactions with chain E, 2 interactions with chain A- Water bridges: E:S.252, A:S.51, A:A.53, E:Y.42, E:G.108, E:N.250, E:S.252, E:T.254, A:S.51, 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
- 5 x CA: CALCIUM ION(Non-covalent)
CA.5: 3 residues within 4Å:- Chain A: E.23
- Chain B: S.191, E.194
5 PLIP interactions:1 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:E.23, H2O.7, H2O.10, H2O.15, H2O.17
CA.9: 3 residues within 4Å:- Chain B: E.23
- Chain C: S.191, E.194
5 PLIP interactions:1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: C:S.191, B:E.23, H2O.19, H2O.24, H2O.26
CA.14: 3 residues within 4Å:- Chain C: E.23
- Chain D: S.191, E.194
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.24, H2O.28, H2O.34
CA.20: 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.37, H2O.38, H2O.46
CA.25: 3 residues within 4Å:- Chain A: S.191, E.194
- 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.1, H2O.43, H2O.47
- 5 x CL: CHLORIDE ION(Non-functional Binders)
CL.6: 2 residues within 4Å:- Chain A: I.157, K.158
Ligand excluded by PLIPCL.10: 3 residues within 4Å:- Chain B: I.157, K.158, A.171
Ligand excluded by PLIPCL.15: 3 residues within 4Å:- Chain C: I.157, K.158, A.171
Ligand excluded by PLIPCL.21: 5 residues within 4Å:- Chain D: I.157, K.158, K.170, A.171, W.186
Ligand excluded by PLIPCL.26: 3 residues within 4Å:- Chain E: I.157, K.158, A.171
Ligand excluded by PLIP- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 7 residues within 4Å:- Chain A: E.194, N.195, R.197, V.228, G.229, P.230, L.231
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.197, A:R.197, A:V.228
EDO.11: 4 residues within 4Å:- Chain B: T.94, F.130, R.262
- Ligands: IPA.13
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.12: 7 residues within 4Å:- Chain B: E.194, N.195, R.197, 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.16: 4 residues within 4Å:- Chain C: T.94, F.130, R.262
- Ligands: IPA.19
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.17: 4 residues within 4Å:- Chain B: E.8, L.10
- Chain C: N.226, R.271
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.271, C:R.271
EDO.18: 8 residues within 4Å:- Chain C: E.194, N.195, R.197, D.224, V.228, G.229, P.230, L.231
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.197, C:R.197, C:G.229
EDO.22: 5 residues within 4Å:- Chain D: L.75, N.76, M.79, G.234, D.235
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:L.75, D:N.76, D:N.76, D:N.76
- Water bridges: D:G.234
EDO.23: 4 residues within 4Å:- Chain D: T.94, F.130, R.262
- Ligands: IPA.24
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.27: 8 residues within 4Å:- Chain E: Q.21, S.91, V.92, K.93, T.219, N.265, V.266, T.267
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:Q.21, E:S.91, E:N.265, E:T.267
EDO.28: 6 residues within 4Å:- Chain E: L.75, N.76, M.79, G.234, D.235
- Ligands: EDO.29
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:L.75, E:N.76, E:N.76, E:N.76
EDO.29: 10 residues within 4Å:- Chain E: N.76, M.79, I.84, L.85, M.86, C.232, K.233, G.234, D.235
- Ligands: EDO.28
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:N.76, E:G.234, E:D.235
- Water bridges: E:W.87
EDO.30: 5 residues within 4Å:- Chain E: T.94, F.130, Q.213, R.262
- Ligands: IPA.31
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:Q.213, E:R.262, E:R.262
- Water bridges: E:V.96
- 5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)
IPA.8: 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:H.128
IPA.13: 7 residues within 4Å:- Chain B: H.128, F.130, Y.199, G.200, S.201, R.262
- Ligands: EDO.11
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:F.130
IPA.19: 7 residues within 4Å:- Chain C: H.128, F.130, Y.199, G.200, S.201, R.262
- Ligands: EDO.16
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:F.130
- Hydrogen bonds: C:H.128
- Water bridges: C:R.262
IPA.24: 7 residues within 4Å:- Chain D: H.128, M.129, F.130, Y.199, G.200, S.201
- Ligands: EDO.23
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:F.130
- Water bridges: D:R.262
IPA.31: 6 residues within 4Å:- Chain E: H.128, F.130, Y.199, G.200, S.201
- Ligands: EDO.30
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 1.48 Å
- Oligo State
- homo-pentamer
- Ligands
- 2 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)
- 2 x BGC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-functional Binders)
- 5 x CA: CALCIUM ION(Non-covalent)
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- 12 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