Research workbench
Crystal structure of murine polyomavirus pta strain VP1 in complex with the GT1A glycan
Analyse Crystal structure of murine polyomavirus pta strain VP1 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CPW
- Type
- protein
- Length
- 1,395 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- Q76TX8
- Ligands
- SIA, GAL, NGA
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | VP1 | protein | 278 | 8% helix, 39% strand | Q76TX8 |
| D | VP1 | protein | 283 | 8% helix, 39% strand | Q76TX8 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 12 copies · chains A, B, C, D, E
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains A, B, C, D, E
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.67 | 0.89 | 31 | empty |
| 2 | 117 | 0.67 | 0.90 | 31 | empty |
| 3 | 127 | 0.66 | 0.89 | 29 | empty |
| 4 | 123 | 0.66 | 0.89 | 30 | empty |
| 5 | 115 | 0.64 | 0.88 | 30 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2258 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2249 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2234 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 2225 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2212 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5CPW · Crystal structure of murine polyomavirus PTA strain VP1 in complex with the GT1a glycan · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q76TX8
- Elsewhere: RCSB PDB 5CPW · PDBe 5CPW · UniProt Q76TX8
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