Research workbench
Jc mad-1 polyomavirus VP1 in complex with GD1A oligosaccharide
Analyse Jc mad-1 polyomavirus VP1 in complex with GD1A oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X16
- Type
- protein
- Length
- 1,287 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- P03089
- Ligands
- SIA, K
- Pockets
- 12 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Major capsid protein VP1 | protein | 258 | 8% helix, 42% strand | P03089 |
| C | Major capsid protein VP1 | protein | 256 | 8% helix, 41% strand | P03089 |
| D | Major capsid protein VP1 | protein | 257 | 8% helix, 42% strand | P03089 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains B, C, D, E
- K · Potassium ion · metal · 3 copies · chains A, B, E, C
- GOL · Glycerol · additive · 9 copies · chains A, E, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.52 | 0.78 | 40 | empty |
| 2 | 201 | 0.51 | 0.77 | 38 | empty |
| 3 | 214 | 0.50 | 0.76 | 30 | EDO, GOL |
| 4 | 299 | 0.50 | 0.73 | 35 | empty |
| 5 | 224 | 0.49 | 0.75 | 31 | EDO |
Interfaces
5 interfaces between chains.
- D–E · 2334 Ų buried · 44 hydrogen bonds · protein-protein
- A–E · 2325 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2318 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2316 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 2315 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 4X16 · JC Mad-1 polyomavirus VP1 in complex with GD1a 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 P03089
- Elsewhere: RCSB PDB 4X16 · PDBe 4X16 · UniProt P03089
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