Research workbench
Complex between the lactococcus lactis fpg and an abasic site containing DNA.
Analyse Complex between the lactococcus lactis fpg and an abasic site containing DNA. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PJJ
- Type
- protein + DNA
- Length
- 299 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*(3DR)P*TP*TP*TP*CP*TP*CP*G)- 3'); DNA…
- EC
- 3.2.2.23
- 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 |
|---|---|---|---|---|---|
| D | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)- 3') | dna | 14 | — | — |
| 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 | 271 | 33% 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 | 699 | 0.72 | 0.79 | 47 | GOL |
| 2 | 367 | 0.65 | 0.80 | 31 | empty |
| 3 | 136 | 0.43 | 0.76 | 21 | GOL |
| 4 | 64 | 0.37 | 0.79 | 16 | empty |
| 5 | 60 | 0.33 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- D–A · 695 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–E · 536 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- E–A · 427 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1PJJ · Complex between the Lactococcus lactis Fpg and an abasic site containing DNA. · 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 1PJJ · PDBe 1PJJ · UniProt P42371
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