Research workbench
Muty adenine glycosylase bound to DNA containing a transition state analog (1N) paired with undamaged dg
Analyse Muty adenine glycosylase bound to DNA containing a transition state analog (1N)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q0C
- Type
- protein + DNA
- Length
- 370 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A/G-specific adenine glycosylase; DNA (5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'); DNA…
- EC
- 3.2.2.31
- UniProt
- P83847
- Ligands
- SF4, CA
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A/G-specific adenine glycosylase (EC 3.2.2.31) | protein | 349 | 46% helix, 13% strand | P83847 |
| B | DNA (5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- CA · Calcium ion · metal · chains A, C
- EDO · 1,2-ethanediol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.77 | 0.80 | 56 | empty |
| 2 | 120 | 0.54 | 0.83 | 28 | empty |
| 3 | 191 | 0.49 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 828 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 809 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 427 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6Q0C · MutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired… · the same entry in another collection · chain A against A, TM-score 1.00
- P83847 · AlphaFold monomer V2.0 prediction for adenine DNA glycosylase (P83847) · 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 P83847
- Elsewhere: RCSB PDB 6Q0C · PDBe 6Q0C · UniProt P83847
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