Research workbench
Cryo-EM structure of DNA-PKCS:DNA
Analyse Cryo-EM structure of DNA-PKCS:DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZH8
- Type
- protein + DNA
- Length
- 3,713 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs; DNA…
- EC
- 2.7.11.1
- UniProt
- P78527
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs (EC 2.7.11.1) | protein | 3694 | 63% helix, 2% strand | P78527 |
| B | DNA (5'-D(P*AP*GP*TP*TP*TP*TP*TP*AP*GP*TP*T)-3') | dna | 11 | — | — |
| C | DNA (5'-D(P*AP*CP*TP*AP*AP*AP*AP*A)-3') | dna | 8 | — | — |
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 | 1072 | 0.87 | 0.88 | 147 | empty |
| 2 | 1114 | 0.85 | 0.86 | 111 | empty |
| 3 | 125 | 0.79 | 0.97 | 23 | empty |
| 4 | 409 | 0.78 | 0.87 | 56 | empty |
| 5 | 630 | 0.78 | 0.83 | 78 | empty |
Interfaces
3 interfaces between chains.
- B–C · 522 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- A–C · 207 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 34 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 6ZH8 · Cryo-EM structure of DNA-PKcs:DNA · the same entry in another collection · chain B against B, 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 6ZH8 · PDBe 6ZH8 · UniProt P78527
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