MolNFT v1 · #115648 · protein
Crystal structure of murine polyomavirus pta strain VP1 in complex with the dslnt glycan
5CPX: “Crystal structure of murine polyomavirus pta strain VP1 in complex with the dslnt glycan”. X-ray diffraction, 3 ligands (GAL, SIA, NAG), 20 pockets (best druggability 0.68). MolNFT v1 #115648 on GenesisL1: 3D structure, binding…
- PDB
- 5CPX
- Type
- protein
- Length
- 1,394 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- Q76TX8
- Ligands
- GAL, SIA, NAG
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | VP1 | protein | 278 | 8% helix, 39% strand | Q76TX8 |
| B | VP1 | protein | 277 | 8% helix, 40% strand | Q76TX8 |
| D | VP1 | protein | 283 | 8% helix, 39% strand | Q76TX8 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, B, C, D, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, D, E
- GOL · Glycerol · additive · 4 copies · chains A, B, 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 | 112 | 0.68 | 0.91 | 29 | empty |
| 2 | 112 | 0.67 | 0.90 | 29 | empty |
| 3 | 109 | 0.67 | 0.90 | 28 | empty |
| 4 | 107 | 0.66 | 0.90 | 28 | empty |
| 5 | 613 | 0.66 | 0.76 | 67 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2274 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 2272 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2254 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2236 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 2226 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5CPX · Crystal structure of murine polyomavirus PTA strain VP1 in complex with the DSLNT 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 5CPX · PDBe 5CPX · UniProt Q76TX8
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