MolNFT v1 · #171812 · protein + DNA
Cryo-EM structure of DNA-pk dimer
6ZHE · DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs: “Cryo-EM structure of DNA-pk dimer”. Electron microscopy, 20 pockets (best druggability 0.91). MolNFT v1 #171812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZHE
- Type
- protein + DNA
- Length
- 9,988 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs; X-ray repair cross-complementing…
- EC
- 2.7.11.1, 3.6.4.-, 4.2.99.-
- UniProt
- P78527, P12956, P13010
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 9 distinct chains · 53% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs (EC 2.7.11.1) | protein | 3768 | 59% helix, 1% strand | P78527 |
| B, G | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 489 | 25% helix, 18% strand | P12956 |
| C | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 705 | 35% helix, 15% strand | P13010 |
| F | DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs (EC 2.7.11.1) | protein | 3731 | 58% helix, 1% strand | P78527 |
| H | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 700 | 37% helix, 16% strand | P13010 |
| J | DNA (25-mer) | dna | 25 | — | — |
| I | DNA (27-mer) | dna | 27 | — | — |
| D | DNA (26-mer) | dna | 26 | — | — |
| E | DNA (28-mer) | dna | 28 | — | — |
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 | 971 | 0.91 | 0.93 | 168 | empty |
| 2 | 1074 | 0.91 | 0.92 | 156 | empty |
| 3 | 875 | 0.90 | 0.93 | 128 | empty |
| 4 | 1147 | 0.90 | 0.92 | 159 | empty |
| 5 | 1043 | 0.90 | 0.92 | 134 | empty |
Interfaces
23 interfaces between chains.
- G–H · 8279 Ų buried · 116 hydrogen bonds · protein-protein
- B–C · 8005 Ų buried · 122 hydrogen bonds · protein-protein
- F–H · 2128 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 1846 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1400 Ų buried · 166 hydrogen bonds · nucleic-nucleic
Compared structures
- 6ZHE · Cryo-EM structure of DNA-PK dimer · the same entry in another collection · chain E against E, TM-score 1.00
- 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
- P13010 · AlphaFold monomer V2.0 prediction for X-ray repair cross- complementing protein 5 (P13010) · a predicted model of the same protein · chain H against A, TM-score 0.72
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 6ZHE · PDBe 6ZHE · UniProt P78527 · UniProt P12956 · UniProt P13010
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