MolNFT v1 · #79021 · protein
Crystal structure of human xlf-XRCC4 complex
3SR2 · DNA repair protein XRCC4: “Crystal structure of human xlf-XRCC4 complex”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #79021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SR2
- Type
- protein
- Length
- 1,432 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein XRCC4; Non-homologous end-joining factor 1
- UniProt
- Q13426, Q9H9Q4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein XRCC4 | protein | 139 | 30% helix, 33% strand | Q13426 |
| B, E, F | DNA repair protein XRCC4 | protein | 140 | 29% helix, 34% strand | Q13426 |
| C | Non-homologous end-joining factor 1 | protein | 218 | 47% helix, 23% strand | Q9H9Q4 |
| D | Non-homologous end-joining factor 1 | protein | 218 | 46% helix, 21% strand | Q9H9Q4 |
| G | Non-homologous end-joining factor 1 | protein | 217 | 43% helix, 22% strand | Q9H9Q4 |
| H | Non-homologous end-joining factor 1 | protein | 220 | 42% helix, 18% strand | Q9H9Q4 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.79 | 0.95 | 31 | empty |
| 2 | 187 | 0.77 | 0.92 | 34 | empty |
| 3 | 179 | 0.76 | 0.91 | 29 | empty |
| 4 | 152 | 0.75 | 0.92 | 32 | empty |
| 5 | 83 | 0.75 | 0.97 | 21 | empty |
Interfaces
10 interfaces between chains.
- G–H · 3515 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 3441 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1045 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1016 Ų buried · 4 hydrogen bonds · protein-protein
- F–G · 543 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3SR2 · Crystal Structure of Human XLF-XRCC4 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 A against A, TM-score 0.98
- Q9H9Q4 · AlphaFold monomer V2.0 prediction for non-homologous end-joining factor 1 (Q9H9Q4) · a predicted model of the same protein · chain G against A, TM-score 0.97
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 Q13426
- Every structure of UniProt Q9H9Q4
- Elsewhere: RCSB PDB 3SR2 · PDBe 3SR2 · UniProt Q13426 · UniProt Q9H9Q4
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