MolNFT v1 · #187486 · protein + DNA
DNA-pk complex of DNA end processing
7SGL · DNA-dependent protein kinase catalytic subunit: “DNA-pk complex of DNA end processing”. Electron microscopy, 4 ligands (ATP, IHP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #187486 on GenesisL1: 3D structure, binding sites…
- PDB
- 7SGL
- Type
- protein + DNA
- Length
- 5,458 residues
- Chains
- 6
- 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.-, 3.1.-.-
- UniProt
- P78527, P12956, P13010, Q96SD1
- Ligands
- ATP, IHP, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 3852 | 64% helix, 2% strand | P78527 |
| B | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 507 | 29% helix, 26% strand | P12956 |
| C | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 631 | 37% helix, 21% strand | P13010 |
| D | Protein artemis (EC 3.1.-.-) | protein | 406 | 24% helix, 21% strand | Q96SD1 |
| E | HAIRPIN_1 | dna | 54 | — | — |
| F | HAIRPIN_1 | dna | 8 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- IHP · Inositol hexakisphosphate · ligand · chains B, C
- MG · Magnesium ion · metal · 3 copies · chains A, D, E
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1144 | 0.86 | 0.87 | 138 | MG, ATP |
| 2 | 739 | 0.84 | 0.88 | 77 | empty |
| 3 | 760 | 0.84 | 0.88 | 80 | empty |
| 4 | 469 | 0.83 | 0.90 | 79 | empty |
| 5 | 1193 | 0.81 | 0.82 | 132 | empty |
Interfaces
11 interfaces between chains.
- B–C · 9452 Ų buried · 85 hydrogen bonds · protein-protein
- A–D · 5141 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 1807 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 946 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–E · 910 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 7SGL · DNA-PK complex of DNA end processing · the same entry in another collection · chain F against F, TM-score 1.00
- Q96SD1 · AlphaFold monomer V2.0 prediction for protein artemis (Q96SD1) · a predicted model of the same protein · chain D against A, TM-score 0.87
- 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 0.82
- 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 0.74
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
- Every structure of UniProt Q96SD1
- Elsewhere: RCSB PDB 7SGL · PDBe 7SGL · UniProt P78527 · UniProt P12956 · UniProt P13010 · UniProt Q96SD1
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