Research workbench
Crystal structure of the ku heterodimer bound to DNA
Analyse Crystal structure of the ku heterodimer 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
- 1JEY
- Type
- protein + DNA
- Length
- 1,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)- 3'); DNA…
- UniProt
- P12956, P13010
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)- 3') | dna | 18 | — | — |
| D | DNA (34-mer) | dna | 31 | — | — |
| A | KU70 | protein | 493 | 33% helix, 27% strand | P12956 |
| B | KU80 | protein | 530 | 34% helix, 26% strand | P13010 |
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.88 | 0.89 | 131 | empty |
| 2 | 296 | 0.73 | 0.86 | 34 | empty |
| 3 | 200 | 0.70 | 0.87 | 37 | empty |
| 4 | 143 | 0.69 | 0.89 | 25 | empty |
| 5 | 161 | 0.57 | 0.82 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 9424 Ų buried · 102 hydrogen bonds · protein-protein
- C–D · 764 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- D–B · 726 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–B · 482 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–A · 471 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 1JEY · Crystal Structure of the Ku heterodimer bound to DNA · the same entry in another collection · chain C against C, TM-score 1.00
- P13010 · AlphaFold monomer V2.0 prediction for X-ray repair cross- complementing protein 5 (P13010) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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
- Elsewhere: RCSB PDB 1JEY · PDBe 1JEY · UniProt P12956 · UniProt P13010
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