Research workbench
Crystal structure of human DNA-dependent protein kinase catalytic subunit (DNA-pkcs)
Analyse Crystal structure of human DNA-dependent protein kinase catalytic subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KGV
- Type
- protein
- Length
- 4,064 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent protein kinase catalytic subunit
- EC
- 2.7.11.1
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 36% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 354 | 54% helix, 0% strand | — |
| B, P | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 283 | 43% helix, 0% strand | — |
| C, Q | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 406 | 36% helix, 0% strand | — |
| D, R | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 182 | 37% helix, 0% strand | — |
| E, S | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 65 | 26% helix, 0% strand | — |
| F, T | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 531 | 29% helix, 0% strand | — |
| X, Y | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 211 | 18% helix, 3% strand | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.76 | 0.79 | 123 | empty |
| 2 | 1193 | 0.76 | 0.78 | 131 | empty |
| 3 | 719 | 0.73 | 0.79 | 93 | empty |
| 4 | 719 | 0.72 | 0.78 | 90 | empty |
| 5 | 766 | 0.72 | 0.78 | 93 | empty |
Interfaces
14 interfaces between chains.
- O–T · 324 Ų buried · 1 hydrogen bond · protein-protein
- F–X · 269 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 258 Ų buried · 1 hydrogen bond · protein-protein
- T–Y · 241 Ų buried · 0 hydrogen bonds · protein-protein
- P–Q · 235 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3KGV · Crystal Structure of Human DNA-dependent Protein Kinase Catalytic Subunit (DNA-PKcs) · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 3KGV · PDBe 3KGV
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