MolNFT v1 · #171809 · protein + DNA
Cryo-EM structure of DNA-pk monomer
6ZHA · DNA-dependent protein kinase catalytic SUBUNIT,DNA…: “Cryo-EM structure of DNA-pk monomer”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #171809 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZHA
- Type
- protein + DNA
- Length
- 4,784 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent protein kinase catalytic SUBUNIT,DNA- dependent protein kinase catalytic…
- EC
- 2.7.11.1, 3.6.4.-, 4.2.99.-
- UniProt
- P78527, P12956, P13010
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 53% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic SUBUNIT,DNA- dependent protein kinase catalytic SUBUNIT,DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs (EC 2.7.11.1) | protein | 3707 | 60% helix, 2% strand | P78527 |
| B | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 489 | 27% helix, 19% strand | P12956 |
| C | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 539 | 30% helix, 19% strand | P13010 |
| D | DNA | dna | 25 | — | — |
| E | DNA | dna | 24 | — | — |
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 | 815 | 0.87 | 0.90 | 100 | empty |
| 2 | 1002 | 0.87 | 0.88 | 124 | empty |
| 3 | 1033 | 0.84 | 0.85 | 107 | empty |
| 4 | 408 | 0.83 | 0.91 | 53 | empty |
| 5 | 320 | 0.82 | 0.92 | 51 | empty |
Interfaces
10 interfaces between chains.
- B–C · 8496 Ų buried · 102 hydrogen bonds · protein-protein
- D–E · 1299 Ų buried · 139 hydrogen bonds · nucleic-nucleic
- A–B · 1201 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 395 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6ZHA · Cryo-EM structure of DNA-PK monomer · the same entry in another collection · chain B against B, 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 0.76
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 6ZHA · PDBe 6ZHA · UniProt P78527 · UniProt P12956 · UniProt P13010
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