Research workbench
Crystal structure of a complex between the wild-type lactococcus lactis fpg (mutm) and a N7-benzyl-fapy-dg containing DNA
Analyse Crystal structure of a complex between the wild-type lactococcus lactis fpg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C58
- Type
- protein + DNA
- Length
- 297 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA glycosylase; DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS)…
- EC
- 4.2.99.18
- UniProt
- P42371
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA glycosylase (EC 4.2.99.18) | protein | 269 | 33% helix, 23% strand | P42371 |
| B | DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS) P*DTP*DTP*DTP*DCP*DTP*DCP*DG)-3') | dna | 14 | — | — |
| C | DNA (5'- D(*DGP*DCP*DGP*DAP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DGP*DA)-3') | dna | 14 | — | — |
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 | 639 | 0.72 | 0.79 | 43 | empty |
| 2 | 73 | 0.61 | 0.90 | 22 | empty |
| 3 | 218 | 0.45 | 0.73 | 30 | empty |
| 4 | 83 | 0.33 | 0.74 | 15 | empty |
| 5 | 54 | 0.30 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 878 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 545 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–C · 421 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3C58 · Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a… · the same entry in another collection · chain A against A, TM-score 1.00
- P42371 · AlphaFold monomer V2.0 prediction for formamidopyrimidine-DNA glycosylase (P42371) · a predicted model of the same protein · chain A against A, 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 P42371
- Elsewhere: RCSB PDB 3C58 · PDBe 3C58 · UniProt P42371
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.