Research workbench
Mutm crosslinked to undamaged DNA sampling A:T base pair IC2
Analyse Mutm crosslinked to undamaged DNA sampling A:T base pair IC2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F5P
- Type
- protein + DNA
- Length
- 279 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*TP*GP*GP*AP*CP*GP*C)-3'…
- EC
- 3.2.2.23
- UniProt
- P84131
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3' | dna | 13 | — | — |
| D | 5'-D(*TP*GP*CP*G*TP*CP*CP*AP*AP*GP*TP*CP*TP*AP*CP*C)-3' | dna | 12 | — | — |
| A | Formamidopyrimidine-DNA glycosidase (EC 3.2.2.23) | protein | 254 | 30% helix, 26% 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.68 | 0.79 | 42 | empty |
| 2 | 147 | 0.46 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- D–A · 649 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 550 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–A · 483 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2F5P · MutM crosslinked to undamaged DNA sampling A:T base pair IC2 · the same entry in another collection · chain C against C, 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 2F5P · PDBe 2F5P · UniProt P84131
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