Research workbench
Crystal structure of papillomavirus E1 hexameric helicase with ssdna and mgadp
Analyse Crystal structure of papillomavirus E1 hexameric helicase with ssdna and mgadp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GXA
- Type
- protein + DNA
- Length
- 3,264 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'; Replication protein E1
- UniProt
- P03116
- Ligands
- ADP, MG, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | dna | 6 | — | — |
| N | 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' | dna | 7 | — | — |
| A, B, C, D, F, G, I, J, L | Replication protein E1 | protein | 270 | 47% helix, 10% strand | P03116 |
| E, H | Replication protein E1 | protein | 274 | 49% helix, 11% strand | P03116 |
| K | Replication protein E1 | protein | 273 | 49% helix, 11% strand | P03116 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 11 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 3 copies · chains A, B, C, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.84 | 0.85 | 131 | empty |
| 2 | 859 | 0.82 | 0.84 | 109 | empty |
| 3 | 863 | 0.81 | 0.84 | 95 | MG, ADP |
| 4 | 774 | 0.80 | 0.84 | 76 | empty |
| 5 | 543 | 0.80 | 0.86 | 66 | empty |
Interfaces
32 interfaces between chains.
- B–C · 1647 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 1646 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1625 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1621 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1513 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2GXA · Crystal structure of papillomavirus E1 hexameric helicase with ssDNA and MgADP · the same entry in another collection · chain M against M, 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 2GXA · PDBe 2GXA · UniProt P03116
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