MolNFT v1 · #14063 · protein + DNA
Borohydride-trapped HOGG1 intermediate structure co- crystallized with 8-aminoguanine
1LWV · 5'- D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3': “Borohydride-trapped HOGG1 intermediate structure co- crystallized with 8-aminoguanine”. X-ray diffraction, 2 ligands (ANG, CA), 5 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 1LWV
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'; 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED)…
- EC
- 3.2.2.-
- UniProt
- O15527
- Ligands
- ANG, CA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'- D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | dna | 15 | — | — |
| E | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(PED) P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 15 | — | — |
| A | 8-oxoguanine DNA glycosylase (EC 3.2.2.-) | protein | 314 | 48% helix, 11% strand | O15527 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.73 | 0.99 | 23 | ANG |
| 2 | 453 | 0.61 | 0.76 | 39 | CA |
| 3 | 101 | 0.49 | 0.81 | 16 | empty |
| 4 | 153 | 0.44 | 0.76 | 27 | empty |
| 5 | 53 | 0.26 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- E–A · 649 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–E · 627 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- D–A · 440 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1LWV · Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-aminoguanine · the same entry in another collection · chain D against D, TM-score 1.00
- O15527 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (O15527) · 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 O15527
- Elsewhere: RCSB PDB 1LWV · PDBe 1LWV · UniProt O15527
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