Research workbench
X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain
Analyse X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K75
- Type
- protein
- Length
- 791 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein XRCC1; DNA polymerase beta
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P18887, P06766
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA repair protein XRCC1 | protein | 151 | 11% helix, 45% strand | P18887 |
| C | DNA repair protein XRCC1 | protein | 149 | 6% helix, 38% strand | P18887 |
| D | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 248 | 44% helix, 17% strand | P06766 |
| E | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 243 | 43% helix, 19% strand | P06766 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.66 | 0.79 | 66 | empty |
| 2 | 126 | 0.50 | 0.80 | 24 | empty |
| 3 | 72 | 0.43 | 0.81 | 18 | empty |
| 4 | 125 | 0.39 | 0.74 | 24 | empty |
| 5 | 55 | 0.33 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- D–E · 685 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 647 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 631 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3K75 · X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain · the same entry in another collection · chain E against E, TM-score 1.00
- P18887 · AlphaFold monomer V2.0 prediction for DNA repair protein XRCC1 (P18887) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P06766 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06766) · a predicted model of the same protein · chain D against A, TM-score 0.89
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 P18887
- Every structure of UniProt P06766
- Elsewhere: RCSB PDB 3K75 · PDBe 3K75 · UniProt P18887 · UniProt P06766
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