MolNFT v1 · #66792 · protein + DNA
Crystal structure of clostridium acetobutylicum 8-oxoguanine GLYCOSYLASE/LYASE in complex with dsdna containing adenine opposite to 8-oxog
3I0X · 8-oxoguanine-DNA-glycosylase: “Crystal structure of clostridium acetobutylicum 8-oxoguanine GLYCOSYLASE/LYASE in complex with dsdna…”. X-ray diffraction, 1 ligand (NA), 1 pocket (best druggability 0.59). MolNFT v1 #66792 on…
- PDB
- 3I0X
- Type
- protein + DNA
- Length
- 316 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8-oxoguanine-DNA-glycosylase; 5'-D(*AP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q97FM4
- Ligands
- NA
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 8-oxoguanine-DNA-glycosylase (EC 3.2.2.-, 4.2.99.18) | protein | 291 | 52% helix, 12% strand | Q97FM4 |
| C | 5'-D(*AP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 13 | — | — |
| D | 5'-D(*GP*GP*TP*AP*GP*AP*CP*AP*TP*GP*GP*A)-3' | dna | 12 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.59 | 0.75 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–C · 892 Ų buried · 31 hydrogen bonds · protein-nucleic
- C–D · 526 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–D · 432 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3I0X · Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex… · 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 Q97FM4
- Elsewhere: RCSB PDB 3I0X · PDBe 3I0X · UniProt Q97FM4
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