MolNFT v1 · #184981 · protein + DNA
Crystal structure of a trapped pab-AGOG/DOUBLE-standed DNA covalent intermediate (DNA containing adenine opposite to lesion)
7P9Z · N-GLYCOSYLASE/DNA lyase: “Crystal structure of a trapped pab-AGOG/DOUBLE-standed DNA covalent intermediate (DNA containing adenine…”. X-ray diffraction, 2 pockets (best druggability 0.63). MolNFT v1 #184981 on GenesisL1: 3D…
- PDB
- 7P9Z
- 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)*TP*TP*TP*CP*T)-3'); DNA…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q9UZY0
- Pockets
- 2 · best druggability 0.63
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)*TP*TP*TP*CP*T)-3') | dna | 9 | — | — |
| I | DNA (5'-D(*AP*GP*AP*AP*AP*AP*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 | 226 | 0.63 | 0.82 | 35 | empty |
| 2 | 62 | 0.27 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 562 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–I · 356 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- A–I · 313 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7P9Z · 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 7P9Z · PDBe 7P9Z · UniProt Q9UZY0
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