Research workbench
Catalytically inactive (E3Q) mutm crosslinked to OXOG:C containing DNA CC1
Analyse Catalytically inactive (E3Q) mutm crosslinked to OXOG:C containing DNA CC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F5S
- Type
- protein + DNA
- Length
- 296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3'…
- EC
- 3.2.2.23
- UniProt
- P84131
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3' | dna | 12 | — | — |
| C | 5'-D(*TP*GP*C*GP*TP*CP*CP*(8OG)P*AP*GP*TP*CP*TP*AP*CP*C)- 3' | dna | 11 | — | — |
| A | Formamidopyrimidine-DNA glycosidase (EC 3.2.2.23) | protein | 273 | 29% helix, 25% strand | P84131 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.68 | 0.79 | 40 | empty |
| 2 | 176 | 0.43 | 0.74 | 23 | empty |
| 3 | 124 | 0.43 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–A · 803 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 451 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–A · 450 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2F5S · Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC1 · the same entry in another collection · chain B against B, TM-score 1.00
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 P84131
- Elsewhere: RCSB PDB 2F5S · PDBe 2F5S · UniProt P84131
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