MolNFT v1 · #179296 · protein
Re-refined crystal structure of DNA-dependent protein kinase catalytic subunit complexed with KU80 C-terminal helix
7K17: “Re-refined crystal structure of DNA-dependent protein kinase catalytic subunit complexed with KU80 C-terminal…”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #179296 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7K17
- Type
- protein
- Length
- 7,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent protein kinase catalytic subunit; X-ray repair cross-complementing protein 5
- EC
- 2.7.11.1, 3.6.4.-
- UniProt
- P13010
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 3629 | 57% helix, 1% strand | — |
| B | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 3645 | 57% helix, 1% strand | — |
| D, C | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 9 | 78% helix, 0% strand | P13010 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.86 | 0.89 | 115 | empty |
| 2 | 900 | 0.86 | 0.87 | 104 | empty |
| 3 | 841 | 0.86 | 0.88 | 116 | empty |
| 4 | 753 | 0.85 | 0.88 | 82 | empty |
| 5 | 521 | 0.79 | 0.86 | 73 | empty |
Interfaces
3 interfaces between chains.
- B–D · 479 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 424 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 382 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7K17 · Re-refined crystal structure of DNA-dependent protein kinase catalytic subunit complexed… · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.83
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 P13010
- Elsewhere: RCSB PDB 7K17 · PDBe 7K17 · UniProt P13010
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