MolNFT v1 · #51512 · protein
Crystal structure of papillomavirus E1 hexameric helicase DNA-free form
2V9P · Replication protein E1: “Crystal structure of papillomavirus E1 hexameric helicase DNA-free form”. X-ray diffraction, 2 ligands (MG, PO4), 20 pockets (best druggability 0.81). MolNFT v1 #51512 on GenesisL1: 3D structure, binding…
- PDB
- 2V9P
- Type
- protein
- Length
- 3,236 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication protein E1
- EC
- 3.6.1.-
- UniProt
- P03116
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication protein E1 (EC 3.6.1.-) | protein | 272 | 49% helix, 10% strand | P03116 |
| B, H | Replication protein E1 (EC 3.6.1.-) | protein | 268 | 51% helix, 10% strand | P03116 |
| C, L | Replication protein E1 (EC 3.6.1.-) | protein | 267 | 54% helix, 10% strand | P03116 |
| D | Replication protein E1 (EC 3.6.1.-) | protein | 274 | 52% helix, 10% strand | P03116 |
| E | Replication protein E1 (EC 3.6.1.-) | protein | 270 | 54% helix, 11% strand | P03116 |
| F, K | Replication protein E1 (EC 3.6.1.-) | protein | 269 | 51% helix, 11% strand | P03116 |
| G | Replication protein E1 (EC 3.6.1.-) | protein | 270 | 52% helix, 11% strand | P03116 |
| I | Replication protein E1 (EC 3.6.1.-) | protein | 270 | 51% helix, 10% strand | P03116 |
| J | Replication protein E1 (EC 3.6.1.-) | protein | 272 | 51% helix, 11% strand | P03116 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, G, H, I, J
- PO4 · Phosphate ion · ion · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.81 | 0.84 | 82 | empty |
| 2 | 742 | 0.78 | 0.82 | 76 | empty |
| 3 | 943 | 0.78 | 0.80 | 74 | empty |
| 4 | 733 | 0.78 | 0.82 | 62 | empty |
| 5 | 582 | 0.76 | 0.83 | 55 | empty |
Interfaces
17 interfaces between chains.
- A–B · 1990 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1926 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1920 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 1905 Ų buried · 29 hydrogen bonds · protein-protein
- I–J · 1896 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2V9P · Crystal structure of papillomavirus E1 hexameric helicase DNA-free form · 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 P03116
- Elsewhere: RCSB PDB 2V9P · PDBe 2V9P · UniProt P03116
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