Research workbench
Crystal structure of a trapped pab-AGOG/DOUBLE-standed DNA covalent intermediate (DNA containing cytosine opposite to lesion)
Analyse Crystal structure of a trapped pab-AGOG/DOUBLE-standed DNA covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OY7
- Type
- protein + DNA
- Length
- 260 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-GLYCOSYLASE/DNA lyase; DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3'); DNA…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q9UZY0
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 242 | 70% helix, 0% strand | Q9UZY0 |
| B | DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3') | dna | 9 | — | — |
| I | DNA (5'-D(*AP*GP*AP*AP*AP*CP*AP*AP*A)-3') | dna | 9 | — | — |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.70 | 0.85 | 35 | empty |
| 2 | 66 | 0.28 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 619 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–I · 346 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- A–I · 287 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7OY7 · Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UZY0 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (Q9UZY0) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9UZY0
- Elsewhere: RCSB PDB 7OY7 · PDBe 7OY7 · UniProt Q9UZY0
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