MolNFT v1 · #22715 · protein + DNA
Crystal structure complex between the lactococcus lactis fpg (mutm) and a fapy-dg containing DNA
1TDZ · 5'-D(*CP*TP*CP*TP*TP*TP*(FOX)P*TP*TP*TP*CP*TP*CP*G)-3': “Crystal structure complex between the lactococcus lactis fpg (mutm) and a fapy-dg containing DNA”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.71). MolNFT…
- PDB
- 1TDZ
- Type
- protein + DNA
- Length
- 293 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*TP*CP*TP*TP*TP*(FOX)P*TP*TP*TP*CP*TP*CP*G)-3'…
- EC
- 3.2.2.23
- UniProt
- P42371
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*CP*TP*CP*TP*TP*TP*(FOX)P*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*GP*A)-3' | dna | 14 | — | — |
| A | Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23) | protein | 265 | 34% helix, 23% strand | P42371 |
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 | 624 | 0.71 | 0.79 | 44 | empty |
| 2 | 140 | 0.63 | 0.86 | 21 | empty |
| 3 | 132 | 0.41 | 0.75 | 22 | GOL |
| 4 | 65 | 0.34 | 0.77 | 15 | empty |
| 5 | 61 | 0.27 | 0.73 | 10 | empty |
Interfaces
3 interfaces between chains.
- B–A · 836 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 548 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- C–A · 423 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1TDZ · Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG… · the same entry in another collection · chain B against B, 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 1TDZ · PDBe 1TDZ · UniProt P42371
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