MolNFT v1 · #99721 · protein
Structure of unliganded B-lymphotropic polyomavirus VP1
4MBX · Major capsid protein VP1: “Structure of unliganded B-lymphotropic polyomavirus VP1”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.68). MolNFT v1 #99721 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4MBX
- Type
- protein
- Length
- 2,750 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- Ligands
- CA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Major capsid protein VP1 | protein | 277 | 4% helix, 42% strand | — |
| B, C, J | Major capsid protein VP1 | protein | 276 | 4% helix, 42% strand | — |
| D, I | Major capsid protein VP1 | protein | 275 | 4% helix, 42% strand | — |
| F, H | Major capsid protein VP1 | protein | 274 | 4% helix, 42% strand | — |
| G | Major capsid protein VP1 | protein | 270 | 4% helix, 41% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- EDO · 1,2-ethanediol · additive · 27 copies · chains A, F, B, J, C, D, E, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.68 | 0.78 | 71 | EDO |
| 2 | 427 | 0.66 | 0.79 | 64 | EDO |
| 3 | 403 | 0.64 | 0.79 | 61 | empty |
| 4 | 386 | 0.64 | 0.79 | 56 | EDO |
| 5 | 379 | 0.64 | 0.79 | 56 | empty |
Interfaces
25 interfaces between chains.
- I–J · 2469 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 2459 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2456 Ų buried · 45 hydrogen bonds · protein-protein
- F–J · 2456 Ų buried · 44 hydrogen bonds · protein-protein
- A–E · 2455 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4MBX · Structure of unliganded B-Lymphotropic Polyomavirus VP1 · 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
- Elsewhere: RCSB PDB 4MBX · PDBe 4MBX
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