Research workbench
Very-short-patch DNA repair endonuclease bound to its reaction product site
Analyse Very-short-patch DNA repair endonuclease bound to its reaction product site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ODG
- Type
- protein + DNA
- Length
- 158 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA mismatch endonuclease; 5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3'
- UniProt
- P09184
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch endonuclease | protein | 134 | 37% helix, 17% strand | P09184 |
| F, W | 5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3' | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.70 | 0.77 | 58 | empty |
| 2 | 122 | 0.43 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- F–W · 456 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- A–F · 432 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–W · 260 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1ODG · Very-short-patch DNA repair endonuclease bound to its reaction product site · the same entry in another collection · chain A against A, TM-score 1.00
- P09184 · AlphaFold monomer V2.0 prediction for very short patch repair protein (P09184) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P09184
- Elsewhere: RCSB PDB 1ODG · PDBe 1ODG · UniProt P09184
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