Research workbench
MutM containing F114A mutation bound to oxoG-containing DNA
Analyse MutM containing F114A mutation bound to oxoG-containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G4R
- Type
- protein + DNA
- Length
- 278 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Geobacillus stearothermophilus; SYNTHETIC CONSTRUCT
- Molecule
- Formamidopyrimidine-DNA glycosylase; DNA (5'-D(P*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP…
- EC
- 3.2.2.23
- UniProt
- P84131
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.95 · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23) | protein | 252 | 31% helix, 26% strand | P84131 |
| B | DNA (5'-D(P*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3') | dna | 14 | — | — |
| C | DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG)P*AP*GP*(TX2)P*CP*TP*AP*CP*C)-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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.68 | 0.78 | 45 | empty |
| 2 | 162 | 0.55 | 0.81 | 24 | empty |
| 3 | 63 | 0.25 | 0.72 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 717 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 528 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- A–B · 396 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4G4R · Mutm containing F114A mutation bound to oxog-containing DNA · 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
- Every structure of UniProt P84131
- Elsewhere: RCSB PDB 4G4R · PDBe 4G4R · UniProt P84131
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