MolNFT v1 · #54791 · protein + DNA
Crystal structure of a complex between the wild-type lactococcus lactis fpg (mutm) and an oxidized pyrimidine containing DNA at 310K
2XZU · Formamidopyrimidine-DNA glycosylase: “Crystal structure of a complex between the wild-type lactococcus lactis fpg (mutm) and an oxidized pyrimidine…”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 2XZU
- Type
- protein + DNA
- Length
- 294 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidine-DNA glycosylase; 5'-D(*CP*TP*CP*TP*TP*TP*VETP*TP*TP*TP*CP*TP*CP*G)-3'…
- EC
- 3.2.2.23, 4.2.99.18
- UniProt
- P42371
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.71
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 | 266 | 33% helix, 23% strand | P42371 |
| B | 5'-D(*CP*TP*CP*TP*TP*TP*VETP*TP*TP*TP*CP*TP*CP*G)-3' | dna | 14 | — | — |
| C | 5'-D(GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*G*A)-3' | dna | 14 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.71 | 0.79 | 43 | empty |
| 2 | 76 | 0.54 | 0.86 | 19 | empty |
| 3 | 103 | 0.37 | 0.75 | 15 | empty |
| 4 | 63 | 0.34 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 772 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 544 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–C · 423 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2XZU · Crystal structure of a complex between the wild-type lactococcus lactis fpg (mutm) and an… · 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 2XZU · PDBe 2XZU · UniProt P42371
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