Research workbench
Cryo-EM structure of human DNA-pk holoenzyme
Analyse Cryo-EM structure of human DNA-pk holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y3R
- Type
- protein + DNA
- Length
- 4,740 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- X-ray repair cross-complementing protein 6; X-ray repair cross-complementing protein 5…
- EC
- 3.6.4.-, 4.2.99.-, 2.7.11.1
- UniProt
- P12956, P13010, P78527
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 6 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 493 | 30% helix, 18% strand | P12956 |
| B | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 526 | 30% helix, 21% strand | P13010 |
| K | Prkdc-helix | protein | 15 | 80% helix, 0% strand | — |
| D | DNA (34-mer) | dna | 34 | — | — |
| E | DNA (36-mer) | dna | 36 | — | — |
| C | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 3636 | 64% helix, 1% strand | P78527 |
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 | 925 | 0.91 | 0.93 | 159 | empty |
| 2 | 1146 | 0.88 | 0.89 | 145 | empty |
| 3 | 513 | 0.87 | 0.93 | 94 | empty |
| 4 | 451 | 0.85 | 0.92 | 79 | empty |
| 5 | 369 | 0.85 | 0.94 | 73 | empty |
Interfaces
12 interfaces between chains.
- A–B · 8183 Ų buried · 153 hydrogen bonds · protein-protein
- D–E · 1624 Ų buried · 225 hydrogen bonds · nucleic-nucleic
- A–C · 1044 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 650 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–D · 505 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 5Y3R · Cryo-EM structure of Human DNA-PK Holoenzyme · 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 B 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 A against A, TM-score 0.78
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 P12956
- Every structure of UniProt P13010
- Every structure of UniProt P78527
- Elsewhere: RCSB PDB 5Y3R · PDBe 5Y3R · UniProt P12956 · UniProt P13010 · UniProt P78527
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