MolNFT v1 · #150669 · protein + DNA
Crystal structure of the complex between the lactococcus lactis fpg mutant G226P and a fapy-dg containing DNA
6H0S · Formamidopyrimidine-DNA glycosylase: “Crystal structure of the complex between the lactococcus lactis fpg mutant G226P and a fapy-dg containing DNA”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 6H0S
- Type
- protein + DNA
- Length
- 299 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidine-DNA glycosylase; DNA (5'-D(*CP*TP*CP*TP*TP*TP*(FOX)P*TP*TP*TP*CP*TP*CP…
- EC
- 3.2.2.23, 4.2.99.18
- UniProt
- A0A165FVI1
- 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 | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23, 4.2.99.18) | protein | 271 | 33% helix, 23% strand | A0A165FVI1 |
| B | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(FOX)P*TP*TP*TP*CP*TP*CP*G)- 3') | dna | 14 | — | — |
| C | DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-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 | 620 | 0.72 | 0.79 | 45 | empty |
| 2 | 87 | 0.70 | 0.94 | 23 | empty |
| 3 | 243 | 0.48 | 0.74 | 26 | empty |
| 4 | 140 | 0.42 | 0.75 | 20 | GOL |
| 5 | 51 | 0.30 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 844 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 546 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–C · 406 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6H0S · Crystal structure of the complex between the Lactococcus lactis FPG mutant G226P and a… · the same entry in another collection · 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 A0A165FVI1
- Elsewhere: RCSB PDB 6H0S · PDBe 6H0S · UniProt A0A165FVI1
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