Research workbench
Cryo-EM structure of DNA-pkcs in complex with NU7441
Analyse Cryo-EM structure of DNA-pkcs in complex with NU7441 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OTM
- Type
- protein
- Length
- 3,656 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs
- EC
- 2.7.11.1
- UniProt
- P78527
- Ligands
- 2R4
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 62% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs (EC 2.7.11.1) | protein | 3656 | 62% helix, 1% strand | P78527 |
Ligands and binding sites
- 2R4 · 8-(dibenzo[b,d]thiophen-4-yl)-2-(morpholin-4-yl)-4H-chromen-4-one · ligand · chains A
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 | 915 | 0.85 | 0.87 | 100 | empty |
| 2 | 990 | 0.84 | 0.85 | 100 | empty |
| 3 | 1089 | 0.80 | 0.82 | 115 | 2R4 |
| 4 | 151 | 0.78 | 0.94 | 25 | empty |
| 5 | 769 | 0.77 | 0.81 | 96 | empty |
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 7OTM · PDBe 7OTM · UniProt P78527
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