- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.71 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x GAL- NGA- GAL- SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose
- 14 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 4 residues within 4Å:- Chain A: N.22, R.24, Y.41
- Chain B: K.172
8 PLIP interactions:2 interactions with chain B, 6 interactions with chain A- Water bridges: B:K.172, A:N.22, A:R.24, A:R.24, A:R.24
- Salt bridges: B:K.172, A:R.24
- Hydrogen bonds: A:N.22
SO4.11: 3 residues within 4Å:- Chain A: D.141, K.183, K.201
4 PLIP interactions:4 interactions with chain A- Water bridges: A:E.138, A:K.183
- Salt bridges: A:K.183, A:K.201
SO4.15: 4 residues within 4Å:- Chain B: N.22, R.24, Y.41
- Chain C: K.172
9 PLIP interactions:6 interactions with chain B, 3 interactions with chain C- Hydrogen bonds: B:N.22, B:Y.41
- Water bridges: B:F.20, B:N.22, B:Y.41, C:K.172, C:K.172
- Salt bridges: B:R.24, C:K.172
SO4.17: 3 residues within 4Å:- Chain B: D.141, K.183, K.201
5 PLIP interactions:5 interactions with chain B- Water bridges: B:E.138, B:E.138, B:K.183
- Salt bridges: B:K.183, B:K.201
SO4.18: 3 residues within 4Å:- Chain B: K.154, E.155, E.156
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.155, B:E.156
- Water bridges: B:N.60
SO4.21: 4 residues within 4Å:- Chain C: N.22, R.24, Y.41
- Chain D: K.172
8 PLIP interactions:5 interactions with chain C, 3 interactions with chain D- Hydrogen bonds: C:N.22, C:Y.41, C:Y.41
- Water bridges: C:N.22, D:K.172, D:K.172
- Salt bridges: C:R.24, D:K.172
SO4.24: 3 residues within 4Å:- Chain C: D.141, K.183, K.201
5 PLIP interactions:5 interactions with chain C- Water bridges: C:E.138, C:E.138, C:K.183
- Salt bridges: C:K.183, C:K.201
SO4.25: 3 residues within 4Å:- Chain C: K.154, E.155, E.156
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:E.155, C:E.156
- Water bridges: C:N.60
SO4.30: 4 residues within 4Å:- Chain D: N.22, R.24, Y.41
- Chain E: K.172
7 PLIP interactions:4 interactions with chain D, 3 interactions with chain E- Hydrogen bonds: D:N.22
- Water bridges: D:N.22, D:R.24, E:K.172, E:K.172
- Salt bridges: D:R.24, E:K.172
SO4.31: 3 residues within 4Å:- Chain D: D.141, K.183, K.201
3 PLIP interactions:3 interactions with chain D- Water bridges: D:K.183
- Salt bridges: D:K.183, D:K.201
SO4.32: 3 residues within 4Å:- Chain D: K.154, E.155, E.156
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:E.155, D:E.156
- Water bridges: D:N.60, D:E.155, D:E.156
SO4.35: 4 residues within 4Å:- Chain A: K.172
- Chain E: N.22, R.24, Y.41
7 PLIP interactions:4 interactions with chain E, 3 interactions with chain A- Hydrogen bonds: E:N.22
- Water bridges: E:N.22, E:R.24, A:K.172, A:K.172
- Salt bridges: E:R.24, A:K.172
SO4.38: 3 residues within 4Å:- Chain E: D.141, K.183, K.201
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:D.141
- Water bridges: E:K.183, E:K.183
- Salt bridges: E:K.183, E:K.201
SO4.39: 3 residues within 4Å:- Chain E: K.154, E.155, E.156
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:E.155, E:E.156
- Water bridges: E:N.60
- Salt bridges: E:K.154
- 20 x GOL: GLYCEROL(Non-functional Binders)
GOL.7: 3 residues within 4Å:- Chain A: K.152, K.162, D.168
Ligand excluded by PLIPGOL.8: 8 residues within 4Å:- Chain A: E.203, N.204, R.206, D.233, V.237, G.238, P.239, L.240
Ligand excluded by PLIPGOL.9: 4 residues within 4Å:- Chain A: T.30, P.31, E.32, S.33
Ligand excluded by PLIPGOL.10: 3 residues within 4Å:- Chain A: S.52, D.53, T.54
Ligand excluded by PLIPGOL.12: 6 residues within 4Å:- Chain A: R.206, D.233, E.234
- Chain E: K.94, T.226, T.228
Ligand excluded by PLIPGOL.13: 4 residues within 4Å:- Chain A: G.59, N.60, N.61, K.154
Ligand excluded by PLIPGOL.14: 6 residues within 4Å:- Chain A: K.94, N.225, T.226
- Chain B: R.206, D.233, E.234
Ligand excluded by PLIPGOL.16: 8 residues within 4Å:- Chain B: E.203, N.204, R.206, D.233, V.237, G.238, P.239, L.240
Ligand excluded by PLIPGOL.19: 5 residues within 4Å:- Chain B: G.59, N.60, N.61, K.154
- Ligands: GAL-NGA-GAL-SIA-SIA.2
Ligand excluded by PLIPGOL.20: 6 residues within 4Å:- Chain B: K.94, T.226, T.228
- Chain C: R.206, D.233, E.234
Ligand excluded by PLIPGOL.22: 8 residues within 4Å:- Chain C: E.203, N.204, R.206, D.233, V.237, G.238, P.239, L.240
Ligand excluded by PLIPGOL.23: 5 residues within 4Å:- Chain C: G.59, N.60, N.61, K.154
- Ligands: GAL-NGA-GAL-SIA-SIA.3
Ligand excluded by PLIPGOL.26: 4 residues within 4Å:- Chain C: T.30, P.31, E.32, S.33
Ligand excluded by PLIPGOL.27: 8 residues within 4Å:- Chain C: K.94, N.225, T.226, L.227, T.228
- Chain D: R.206, D.233, E.234
Ligand excluded by PLIPGOL.28: 5 residues within 4Å:- Chain D: G.59, N.60, N.61, K.154
- Ligands: GAL-NGA-GAL-SIA-SIA.4
Ligand excluded by PLIPGOL.29: 8 residues within 4Å:- Chain D: E.203, N.204, R.206, D.233, V.237, G.238, P.239, L.240
Ligand excluded by PLIPGOL.33: 3 residues within 4Å:- Chain D: P.31, E.32, S.33
Ligand excluded by PLIPGOL.34: 7 residues within 4Å:- Chain D: K.94, N.225, T.226, T.228
- Chain E: R.206, D.233, E.234
Ligand excluded by PLIPGOL.36: 8 residues within 4Å:- Chain E: E.203, N.204, R.206, D.233, V.237, G.238, P.239, L.240
Ligand excluded by PLIPGOL.37: 4 residues within 4Å:- Chain E: G.59, N.60, N.61, K.154
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Buch, M.H. et al., Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity. Plos Pathog. (2015)
- Release Date
- 2015-10-28
- Peptides
- 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 1.71 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x GAL- NGA- GAL- SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose
- 14 x SO4: SULFATE ION(Non-functional Binders)
- 20 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Buch, M.H. et al., Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity. Plos Pathog. (2015)
- Release Date
- 2015-10-28
- Peptides
- Capsid protein VP1: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E