Research workbench
Crystal structure of asfvpolx in complex with DNA enzyme and pb.
Analyse Crystal structure of asfvpolx in complex with DNA enzyme and pb. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XM8
- Type
- protein + DNA
- Length
- 822 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Repair DNA polymerase X; DNA (36-mer); DNA (23-mer)
- EC
- 2.7.7.7
- UniProt
- P42494
- Ligands
- PB, PO4
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Repair DNA polymerase X (EC 2.7.7.7) | protein | 177 | 31% helix, 28% strand | P42494 |
| B, D | Repair DNA polymerase X (EC 2.7.7.7) | protein | 175 | 34% helix, 33% strand | P42494 |
| E, G | DNA (36-mer) | dna | 36 | — | — |
| F, H | DNA (23-mer) | dna | 23 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.69 | 0.97 | 15 | empty |
| 2 | 277 | 0.53 | 0.75 | 38 | empty |
| 3 | 195 | 0.50 | 0.77 | 22 | PB |
| 4 | 269 | 0.46 | 0.72 | 27 | empty |
| 5 | 143 | 0.46 | 0.78 | 20 | empty |
Interfaces
14 interfaces between chains.
- G–H · 1180 Ų buried · 119 hydrogen bonds · nucleic-nucleic
- E–F · 1167 Ų buried · 114 hydrogen bonds · nucleic-nucleic
- A–E · 689 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–G · 618 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–F · 580 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 5XM8 · Crystal structure of AsfvPolX in complex with DNA enzyme and Pb. · 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 P42494
- Elsewhere: RCSB PDB 5XM8 · PDBe 5XM8 · UniProt P42494
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