MolNFT v1 · #14260 · protein + DNA
Crystal structure of HOGG1 D268E mutant with base-excised DNA and 8- aminoguanine
1M3Q · 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3': “Crystal structure of HOGG1 D268E mutant with base-excised DNA and 8- aminoguanine”. X-ray diffraction, 2 ligands (ANG, CA), 7 pockets (best druggability 0.72). MolNFT v1 #14260…
- PDB
- 1M3Q
- 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'…
- EC
- 3.2.2.-
- UniProt
- O15527
- Ligands
- ANG, CA
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | dna | 15 | — | — |
| C | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(DRZ)P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 15 | — | — |
| A | 8-oxoguanine DNA glycosylase (EC 3.2.2.-) | protein | 314 | 49% helix, 12% strand | O15527 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.72 | 0.98 | 21 | ANG |
| 2 | 435 | 0.60 | 0.75 | 37 | CA |
| 3 | 156 | 0.47 | 0.77 | 26 | empty |
| 4 | 74 | 0.41 | 0.79 | 15 | empty |
| 5 | 69 | 0.28 | 0.73 | 10 | empty |
Interfaces
3 interfaces between chains.
- C–A · 661 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 633 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- B–A · 421 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1M3Q · Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine · the same entry in another collection · chain B against B, 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 1M3Q · PDBe 1M3Q · UniProt O15527
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