Research workbench
Crystal structure of mouse mutyh in complex with DNA containing ap site ANALOGUE:8-oxog (form I)
Analyse Crystal structure of mouse mutyh in complex with DNA containing ap site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EF8
- Type
- protein + DNA
- Length
- 427 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine DNA glycosylase; DNA (5'-D(*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3'); DNA…
- EC
- 3.2.2.31
- UniProt
- Q99P21
- Ligands
- SF4, ZN, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine DNA glycosylase (EC 3.2.2.31) | protein | 402 | 49% helix, 12% strand | Q99P21 |
| B | DNA (5'-D(*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.75 | 0.78 | 56 | empty |
| 2 | 241 | 0.68 | 0.85 | 30 | empty |
| 3 | 119 | 0.53 | 0.82 | 24 | empty |
| 4 | 111 | 0.40 | 0.76 | 25 | empty |
| 5 | 89 | 0.34 | 0.74 | 23 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 931 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 880 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 485 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7EF8 · Crystal structure of mouse MUTYH in complex with DNA containing AP site analogue:8-oxoG… · the same entry in another collection · chain A against A, TM-score 1.00
- Q99P21 · AlphaFold monomer V2.0 prediction for adenine DNA glycosylase (Q99P21) · 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 Q99P21
- Elsewhere: RCSB PDB 7EF8 · PDBe 7EF8 · UniProt Q99P21
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.