MolNFT v1 · #70638 · protein
X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta palm thumb domain
3LQC · DNA repair protein XRCC1: “X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta palm thumb domain”. X-ray diffraction, 2 ligands (NA, CO3), 2 pockets (best druggability 0.49). MolNFT v1 #70638 on GenesisL1: 3D structure…
- PDB
- 3LQC
- Type
- protein
- Length
- 345 residues
- Chains
- 2
- 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
- Ligands
- NA, CO3
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein XRCC1 | protein | 151 | 25% helix, 41% strand | P18887 |
| B | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 194 | 36% helix, 22% strand | P06766 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.49 | 0.78 | 26 | empty |
| 2 | 54 | 0.24 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 689 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3LQC · X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain · the same entry in another collection · chain A against A, TM-score 1.00
- P06766 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06766) · a predicted model of the same protein · chain B against A, TM-score 0.90
- P18887 · AlphaFold monomer V2.0 prediction for DNA repair protein XRCC1 (P18887) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 3LQC · PDBe 3LQC · UniProt P18887 · UniProt P06766
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