MolNFT v1 · #179307 · protein + DNA
Cryoem structure of inactivated-form DNA-pk (complex III)
7K1J · DNA-dependent protein kinase catalytic subunit: “Cryoem structure of inactivated-form DNA-pk (complex III)”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #179307 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7K1J
- Type
- protein + DNA
- Length
- 4,674 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 0.85
Structure
electron microscopy · 7 distinct chains · 48% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 3584 | 54% 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 | 28% 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 | 1056 | 0.85 | 0.86 | 118 | empty |
| 2 | 421 | 0.82 | 0.91 | 49 | empty |
| 3 | 258 | 0.79 | 0.91 | 33 | empty |
| 4 | 565 | 0.78 | 0.84 | 65 | empty |
| 5 | 238 | 0.78 | 0.91 | 36 | empty |
Interfaces
17 interfaces between chains.
- B–C · 8725 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 1268 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 758 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- E–F · 613 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–D · 532 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 7K1J · CryoEM structure of inactivated-form DNA-PK (Complex III) · 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 C against A, TM-score 0.95
- 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 7K1J · PDBe 7K1J · UniProt P78527 · UniProt P12956 · UniProt P13010
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