MolNFT v1 · #109379 · protein
Jc polyomavirus genotype 3 VP1 in complex with GD1B oligosaccharide
4X12 · Major capsid protein: “Jc polyomavirus genotype 3 VP1 in complex with GD1B oligosaccharide”. X-ray diffraction, 2 ligands (SIA, K), 11 pockets (best druggability 0.50). MolNFT v1 #109379 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4X12
- Type
- protein
- Length
- 1,287 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P90498
- Ligands
- SIA, K
- Pockets
- 11 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Major capsid protein | protein | 257 | 8% helix, 41% strand | P90498 |
| C | Major capsid protein | protein | 257 | 7% helix, 42% strand | P90498 |
| D, E | Major capsid protein | protein | 258 | 8% helix, 42% strand | P90498 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, E, B, C, D
- K · Potassium ion · metal · 10 copies · chains A, B, E, C, D
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 9 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.50 | 0.76 | 29 | GOL |
| 2 | 221 | 0.50 | 0.76 | 29 | EDO |
| 3 | 222 | 0.50 | 0.75 | 29 | EDO |
| 4 | 281 | 0.49 | 0.74 | 34 | empty |
| 5 | 216 | 0.49 | 0.75 | 31 | EDO |
Interfaces
5 interfaces between chains.
- B–C · 2337 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 2329 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2329 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2326 Ų buried · 42 hydrogen bonds · protein-protein
- A–E · 2316 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4X12 · JC Polyomavirus genotype 3 VP1 in complex with GD1b oligosaccharide · 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 P90498
- Elsewhere: RCSB PDB 4X12 · PDBe 4X12 · UniProt P90498
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