MolNFT v1 · #111390 · protein + DNA
Crystal structure of muty bound to its anti-substrate with the disulfide cross-linker reduced
4YPH · A/G-specific adenine glycosylase: “Crystal structure of muty bound to its anti-substrate with the disulfide cross-linker reduced”. X-ray diffraction, 2 ligands (SF4, NA), 5 pockets (best druggability 0.72). MolNFT v1 #111390 on…
- PDB
- 4YPH
- Type
- protein + DNA
- Length
- 365 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A/G-specific adenine glycosylase; DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')…
- EC
- 3.2.2.-
- UniProt
- P83847
- Ligands
- SF4, NA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A/G-specific adenine glycosylase (EC 3.2.2.-) | protein | 344 | 48% helix, 15% strand | P83847 |
| B | DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(TP*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.72 | 0.84 | 42 | empty |
| 2 | 103 | 0.68 | 0.91 | 25 | empty |
| 3 | 570 | 0.65 | 0.76 | 38 | empty |
| 4 | 159 | 0.56 | 0.82 | 26 | empty |
| 5 | 63 | 0.28 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 878 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 809 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 419 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4YPH · Crystal Structure of MutY bound to its anti-substrate with the disulfide cross-linker… · the same entry in another collection · chain B against B, TM-score 1.00
- P83847 · AlphaFold monomer V2.0 prediction for adenine DNA glycosylase (P83847) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P83847
- Elsewhere: RCSB PDB 4YPH · PDBe 4YPH · UniProt P83847
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