MolNFT v1 · #10219 · protein
Crystal structure of a XRCC4-DNA ligase IV complex
1IK9 · DNA repair protein XRCC4: “Crystal structure of a XRCC4-DNA ligase IV complex”. X-ray diffraction, 3 pockets (best druggability 0.38). MolNFT v1 #10219 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IK9
- Type
- protein
- Length
- 430 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein XRCC4; DNA ligase IV
- EC
- 6.5.1.1
- UniProt
- Q13426, P49917
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein XRCC4 | protein | 207 | 57% helix, 28% strand | Q13426 |
| B | DNA repair protein XRCC4 | protein | 195 | 54% helix, 27% strand | Q13426 |
| C | DNA ligase IV (EC 6.5.1.1) | protein | 28 | 32% helix, 7% strand | P49917 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.38 | 0.77 | 14 | empty |
| 2 | 60 | 0.36 | 0.78 | 19 | empty |
| 3 | 60 | 0.32 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2792 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 485 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1IK9 · Crystal structure of a XRCC4-DNA ligase IV complex · the same entry in another collection · chain A against A, 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 0.90
- P49917 · AlphaFold monomer V2.0 prediction for DNA ligase 4 (P49917) · a predicted model of the same protein · chain C against A, TM-score 0.80
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 P49917
- Elsewhere: RCSB PDB 1IK9 · PDBe 1IK9 · UniProt Q13426 · UniProt P49917
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