MolNFT v1 · #179300 · protein + DNA
Cryoem structure of DNA-pk catalytic subunit complexed with DNA (complex II)
7K1B · DNA-dependent protein kinase catalytic subunit: “Cryoem structure of DNA-pk catalytic subunit complexed with DNA (complex II)”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #179300 on GenesisL1: 3D structure…
- PDB
- 7K1B
- Type
- protein + DNA
- Length
- 3,637 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent protein kinase catalytic subunit; DNA (5'…
- EC
- 2.7.11.1
- UniProt
- P78527
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 57% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 3589 | 57% helix, 1% strand | P78527 |
| D | DNA (5'- D(P*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 | — | — |
| F | DNA (5'- D(P*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 | 8 | — | — |
| G | DNA (5'- D(P*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*AP*TP*GP*C)-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 | 1156 | 0.83 | 0.84 | 109 | empty |
| 2 | 622 | 0.82 | 0.87 | 75 | empty |
| 3 | 794 | 0.82 | 0.85 | 73 | empty |
| 4 | 631 | 0.81 | 0.85 | 86 | empty |
| 5 | 155 | 0.80 | 0.96 | 27 | empty |
Interfaces
5 interfaces between chains.
- D–G · 742 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–D · 682 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–F · 361 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- A–G · 258 Ų buried · 4 hydrogen bonds · protein-nucleic
- F–G · 88 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 7K1B · CryoEM structure of DNA-PK catalytic subunit complexed with DNA (Complex II) · the same entry in another collection · chain D against D, TM-score 1.00
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
- Elsewhere: RCSB PDB 7K1B · PDBe 7K1B · UniProt P78527
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