Research workbench
Crystal structure of asfvpolx in complex with DNA enzyme at P43212 space group
Analyse Crystal structure of asfvpolx in complex with DNA enzyme at P43212 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XMA
- Type
- protein + DNA
- Length
- 407 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Repair DNA polymerase X; DNA (36-mer); DNA/RNA…
- EC
- 2.7.7.7
- UniProt
- P42494
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Repair DNA polymerase X (EC 2.7.7.7) | protein | 174 | 30% helix, 30% strand | P42494 |
| E | DNA (36-mer) | dna | 36 | — | — |
| F | DNA/RNA (5'-D(*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*T)-R(P*G)- D(P*GP*GP*TP*GP*CP*GP*TP*TP*AP*CP*A)-3') | dna | 23 | — | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.79 | 0.93 | 31 | empty |
| 2 | 63 | 0.73 | 0.99 | 16 | empty |
| 3 | 86 | 0.71 | 0.94 | 27 | empty |
| 4 | 126 | 0.49 | 0.80 | 15 | empty |
| 5 | 58 | 0.41 | 0.81 | 13 | empty |
Interfaces
5 interfaces between chains.
- E–F · 1170 Ų buried · 108 hydrogen bonds · nucleic-nucleic
- A–E · 624 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–F · 584 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–F · 361 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–E · 330 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 5XMA · Crystal structure of AsfvPolX in complex with DNA enzyme at P43212 space group · 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 5XMA · PDBe 5XMA · UniProt P42494
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