MolNFT v1 · #65195 · protein + DNA
Mutm encountering an intrahelical 8-oxoguanine (oxog) lesion in EC4- loop deletion complex
3GPU · DNA glycosylase: “Mutm encountering an intrahelical 8-oxoguanine (oxog) lesion in EC4- loop deletion complex”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.65). MolNFT v1 #65195 on GenesisL1: 3D structure…
- PDB
- 3GPU
- Type
- protein + DNA
- Length
- 276 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA glycosylase; DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)- 3'); DNA…
- EC
- 4.2.99.18
- UniProt
- P84131
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA glycosylase (EC 4.2.99.18) | protein | 251 | 31% helix, 26% strand | P84131 |
| B | DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)- 3') | dna | 13 | — | — |
| C | DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG) P*AP*GP*TP*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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.65 | 0.78 | 40 | empty |
| 2 | 113 | 0.45 | 0.79 | 23 | empty |
| 3 | 147 | 0.43 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 630 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 547 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–B · 431 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3GPU · MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion 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 P84131
- Elsewhere: RCSB PDB 3GPU · PDBe 3GPU · UniProt P84131
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