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
- 6ERH
- Type
- protein + DNA
- Length
- 2,169 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 0.89
Structure
x-ray diffraction · 9 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 | 490 | 32% helix, 26% strand | P12956 |
| B | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 534 | 34% helix, 26% strand | P13010 |
| C | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 493 | 32% helix, 25% strand | P12956 |
| D | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 535 | 34% helix, 26% strand | P13010 |
| F | DNA (34-mer) | dna | 32 | — | — |
| K, R | DNA (21-mer) | dna | 21 | — | — |
| M | Non-homologous end-joining factor 1 | protein | 7 | 0% helix, 0% strand | Q9H9Q4 |
| O | DNA (34-mer) | dna | 30 | — | — |
| T | Non-homologous end-joining factor 1 | protein | 6 | 0% helix, 0% strand | Q9H9Q4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1024 | 0.89 | 0.91 | 114 | empty |
| 2 | 478 | 0.84 | 0.91 | 66 | empty |
| 3 | 351 | 0.82 | 0.92 | 40 | empty |
| 4 | 709 | 0.80 | 0.84 | 67 | empty |
| 5 | 898 | 0.78 | 0.81 | 68 | empty |
Interfaces
20 interfaces between chains.
- C–D · 10030 Ų buried · 107 hydrogen bonds · protein-protein
- A–B · 9928 Ų buried · 106 hydrogen bonds · protein-protein
- B–F · 1122 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–O · 1121 Ų buried · 12 hydrogen bonds · protein-nucleic
- O–R · 938 Ų buried · 89 hydrogen bonds · nucleic-nucleic
Compared structures
- 6ERH · Complex of XLF and heterodimer Ku bound to DNA · the same entry in another collection · chain T against T, 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 6ERH · PDBe 6ERH · UniProt P12956 · UniProt P13010 · UniProt Q9H9Q4
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