MolNFT v1 · #18271 · protein + DNA
Crystal structure of wild type lactococcus lactis fpg complexed to a 1,3 propanediol containing DNA
1PJI · DNA (5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)…: “Crystal structure of wild type lactococcus lactis fpg complexed to a 1,3 propanediol containing DNA”. X-ray diffraction, 2 ligands (PDI, ZN), 3 pockets (best druggability…
- PDB
- 1PJI
- Type
- protein + DNA
- Length
- 294 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)- 3'); DNA…
- EC
- 3.2.2.23
- UniProt
- P42371
- Ligands
- PDI, ZN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)- 3') | dna | 13 | — | — |
| E | DNA (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 | 267 | 34% helix, 24% strand | P42371 |
Ligands and binding sites
- PDI · Phosphoric acid mono-(3-hydroxy-propyl) ester · ligand · chains D, A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains D, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.72 | 0.79 | 43 | GOL |
| 2 | 239 | 0.57 | 0.78 | 25 | PDI |
| 3 | 97 | 0.37 | 0.75 | 15 | GOL |
Interfaces
3 interfaces between chains.
- D–A · 614 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–E · 540 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- E–A · 427 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1PJI · Crystal structure of wild type Lactococcus lactis FPG complexed to a 1,3 propanediol… · the same entry in another collection · chain D against D, 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 1PJI · PDBe 1PJI · UniProt P42371
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