Research workbench
Cryoem structure of inactivated-form DNA-pk (complex IV)
Analyse Cryoem structure of inactivated-form DNA-pk (complex IV) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K1K
- Type
- protein + DNA
- Length
- 4,694 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent protein kinase catalytic subunit; X-ray repair cross-complementing protein…
- EC
- 2.7.11.1, 3.6.4.-, 4.2.99.-
- UniProt
- P78527, P12956, P13010
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 49% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 3604 | 56% helix, 1% strand | P78527 |
| B | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 490 | 26% helix, 21% strand | P12956 |
| C | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 526 | 26% helix, 21% strand | P13010 |
| D | DNA (5'- D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP* CP*G)-3') | dna | 24 | — | — |
| E | DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3') | dna | 13 | — | — |
| F | DNA (5'- D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP* CP*G)-3') | dna | 21 | — | — |
| G | DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3') | dna | 16 | — | — |
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 | 928 | 0.86 | 0.88 | 123 | empty |
| 2 | 868 | 0.85 | 0.87 | 101 | empty |
| 3 | 609 | 0.83 | 0.88 | 80 | empty |
| 4 | 519 | 0.83 | 0.89 | 56 | empty |
| 5 | 191 | 0.82 | 0.96 | 56 | empty |
Interfaces
17 interfaces between chains.
- B–C · 8607 Ų buried · 78 hydrogen bonds · protein-protein
- A–B · 1254 Ų buried · 8 hydrogen bonds · protein-protein
- D–G · 753 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–D · 625 Ų buried · 10 hydrogen bonds · protein-nucleic
- E–F · 545 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Compared structures
- 7K1K · CryoEM structure of inactivated-form DNA-PK (Complex IV) · the same entry in another collection · chain G against G, 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 C against A, TM-score 0.94
- P12956 · AlphaFold monomer V2.0 prediction for X-ray repair cross- complementing protein 6 (P12956) · a predicted model of the same protein · chain B against A, TM-score 0.75
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 P78527
- Every structure of UniProt P12956
- Every structure of UniProt P13010
- Elsewhere: RCSB PDB 7K1K · PDBe 7K1K · UniProt P78527 · UniProt P12956 · UniProt P13010
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