Research workbench
Crystal structure of a trapped reaction intermediate of the DNA repair enzyme endonuclease VIII with brominated-DNA
Analyse Crystal structure of a trapped reaction intermediate of the DNA repair enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K3X
- Type
- protein + DNA
- Length
- 273 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU) P*GP*G)-3'…
- EC
- 3.2.2.-
- UniProt
- P50465
- Ligands
- ZN, SO4
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU) P*GP*G)-3' | dna | 10 | — | — |
| C | 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' | dna | 10 | — | — |
| A | Endonuclease VIII (EC 3.2.2.-) | protein | 253 | 32% helix, 24% strand | P50465 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.55 | 0.78 | 26 | empty |
| 2 | 229 | 0.48 | 0.74 | 30 | SO4 |
| 3 | 154 | 0.46 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–A · 610 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 457 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- B–A · 356 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified (nucleotide modification).
Compared structures
- 1K3X · Crystal structure of a trapped reaction intermediate of the DNA repair enzyme… · the same entry in another collection · chain B against B, TM-score 1.00
- P50465 · AlphaFold monomer V2.0 prediction for endonuclease 8 (P50465) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P50465
- Elsewhere: RCSB PDB 1K3X · PDBe 1K3X · UniProt P50465
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