Research workbench
Complex of XLF and heterodimer Ku bound to DNA
Analyse Complex of XLF and heterodimer Ku bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ERG
- Type
- protein + DNA
- Length
- 2,190 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- X-ray repair cross-complementing protein 6; X-ray repair cross-complementing protein 5…
- EC
- 3.6.4.-, 4.2.99.-
- UniProt
- P12956, P13010, Q9H9Q4
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.9 · 8 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 501 | 33% helix, 26% strand | P12956 |
| B | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 531 | 34% helix, 26% strand | P13010 |
| C, F | Non-homologous end-joining factor 1 | protein | 7 | 0% helix, 0% strand | Q9H9Q4 |
| D | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 503 | 33% helix, 26% strand | P12956 |
| E | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 536 | 34% helix, 26% strand | P13010 |
| H, K | DNA (21-mer) | dna | 21 | — | — |
| M | DNA (34-mer) | dna | 32 | — | — |
| R | DNA (34-mer) | dna | 31 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.87 | 0.90 | 94 | empty |
| 2 | 1099 | 0.87 | 0.88 | 88 | empty |
| 3 | 626 | 0.80 | 0.85 | 64 | SO4 |
| 4 | 671 | 0.80 | 0.84 | 69 | SO4 |
| 5 | 277 | 0.79 | 0.92 | 34 | empty |
Interfaces
18 interfaces between chains.
- D–E · 10055 Ų buried · 132 hydrogen bonds · protein-protein
- A–B · 9935 Ų buried · 123 hydrogen bonds · protein-protein
- B–R · 1111 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–M · 1072 Ų buried · 13 hydrogen bonds · protein-nucleic
- K–M · 955 Ų buried · 93 hydrogen bonds · nucleic-nucleic
Compared structures
- 6ERG · Complex of xlf and heterodimer ku bound to DNA · the same entry in another collection · chain R against R, TM-score 1.00
- P12956 · AlphaFold monomer V2.0 prediction for X-ray repair cross- complementing protein 6 (P12956) · a predicted model of the same protein · chain A 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 P12956
- Every structure of UniProt P13010
- Every structure of UniProt Q9H9Q4
- Elsewhere: RCSB PDB 6ERG · PDBe 6ERG · UniProt P12956 · UniProt P13010 · UniProt Q9H9Q4
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