Research workbench
Crystal structure complex between the lactococcus lactis fpg and an abasic site containing DNA
Analyse Crystal structure complex between the lactococcus lactis fpg and an abasic site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NNJ
- Type
- protein + DNA
- Length
- 294 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3'…
- EC
- 3.2.2.23
- UniProt
- P42371
- Ligands
- PDI, ZN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3' | dna | 13 | — | — |
| E | 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 | 33% helix, 23% 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 · 2 copies · chains D, E, A
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 | 700 | 0.72 | 0.79 | 45 | GOL |
| 2 | 341 | 0.65 | 0.80 | 40 | PDI |
| 3 | 126 | 0.40 | 0.75 | 21 | GOL |
Interfaces
3 interfaces between chains.
- D–A · 630 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–E · 538 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- E–A · 421 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1NNJ · Crystal structure Complex between the Lactococcus lactis Fpg and an abasic site… · 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 1NNJ · PDBe 1NNJ · UniProt P42371
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.