MolNFT v1 · #177335 · protein + DNA
Crystal structure of mouse mutyh in complex with DNA containing ap site ANALOGUE:8-oxog (form II)
7EF9 · Adenine DNA glycosylase: “Crystal structure of mouse mutyh in complex with DNA containing ap site ANALOGUE:8-oxog (form II)”. X-ray diffraction, 3 ligands (SF4, ZN, SO4), 7 pockets (best druggability 0.74). MolNFT v1 #177335 on…
- PDB
- 7EF9
- Type
- protein + DNA
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine DNA glycosylase; DNA (5'-D(*AP*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)- 3')…
- EC
- 3.2.2.31
- UniProt
- Q99P21
- Ligands
- SF4, ZN, SO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine DNA glycosylase (EC 3.2.2.31) | protein | 414 | 48% helix, 12% strand | Q99P21 |
| B | DNA (5'-D(*AP*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)- 3') | dna | 14 | — | — |
| C | DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.74 | 0.77 | 63 | empty |
| 2 | 53 | 0.70 | 0.98 | 16 | empty |
| 3 | 166 | 0.59 | 0.83 | 23 | empty |
| 4 | 179 | 0.55 | 0.80 | 33 | empty |
| 5 | 319 | 0.53 | 0.74 | 32 | ZN, SO4 |
Interfaces
3 interfaces between chains.
- A–B · 905 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 903 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 493 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7EF9 · 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 0.96
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 7EF9 · PDBe 7EF9 · UniProt Q99P21
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