Research workbench
Crystal structure of XRCC4/XLF-cernunnos complex
Analyse Crystal structure of XRCC4/XLF-cernunnos complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q4F
- Type
- protein
- Length
- 1,536 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-homologous end-joining factor 1; DNA repair protein XRCC4
- UniProt
- Q9H9Q4, Q13426
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, A, B | Non-homologous end-joining factor 1 | protein | 227 | 48% helix, 25% strand | Q9H9Q4 |
| C, D, G, H | DNA repair protein XRCC4 | protein | 157 | 40% helix, 36% strand | Q13426 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.67 | 0.77 | 70 | empty |
| 2 | 81 | 0.67 | 0.92 | 18 | empty |
| 3 | 69 | 0.65 | 0.92 | 18 | empty |
| 4 | 365 | 0.64 | 0.79 | 49 | empty |
| 5 | 92 | 0.63 | 0.89 | 28 | empty |
Interfaces
13 interfaces between chains.
- A–B · 3537 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 3527 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 1660 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1641 Ų buried · 10 hydrogen bonds · protein-protein
- F–D · 646 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3Q4F · Crystal structure of xrcc4/xlf-cernunnos complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q13426 · AlphaFold monomer V2.0 prediction for DNA repair protein XRCC4 (Q13426) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q9H9Q4 · AlphaFold monomer V2.0 prediction for non-homologous end-joining factor 1 (Q9H9Q4) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q9H9Q4
- Every structure of UniProt Q13426
- Elsewhere: RCSB PDB 3Q4F · PDBe 3Q4F · UniProt Q9H9Q4 · UniProt Q13426
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