Research workbench
Crystal structure of a trapped pab-AGOG/SINGLE-standed DNA covalent intermediate
Analyse Crystal structure of a trapped pab-AGOG/SINGLE-standed DNA covalent intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OUE
- Type
- protein + DNA
- Length
- 999 residues
- Chains
- 8
- 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')
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q9UZY0
- Ligands
- K, PO4
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 242 | 71% helix, 0% strand | Q9UZY0 |
| B, D | DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3') | dna | 8 | — | — |
| F | DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3') | dna | 9 | — | — |
| G | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 241 | 70% helix, 0% strand | Q9UZY0 |
| H | DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3') | dna | 7 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.71 | 0.88 | 32 | empty |
| 2 | 233 | 0.70 | 0.86 | 35 | empty |
| 3 | 299 | 0.68 | 0.83 | 33 | empty |
| 4 | 63 | 0.67 | 0.95 | 18 | empty |
| 5 | 282 | 0.66 | 0.82 | 33 | empty |
Interfaces
11 interfaces between chains.
- C–D · 709 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 698 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 649 Ų buried · 12 hydrogen bonds · protein-nucleic
- G–H · 617 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 524 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 7OUE · Crystal structure of a trapped Pab-AGOG/single-standed DNA covalent intermediate · the same entry in another collection · chain H against H, TM-score 1.00
- Q9UZY0 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (Q9UZY0) · a predicted model of the same protein · chain E 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 Q9UZY0
- Elsewhere: RCSB PDB 7OUE · PDBe 7OUE · UniProt Q9UZY0
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