MolNFT v1 · #103331 · protein + DNA
Crystal structure of a complex between an inhibited llfpg and a N7- benzyl-fapy-dg containing DNA
4PDI · Formamidopyrimidine-DNA glycosylase: “Crystal structure of a complex between an inhibited llfpg and a N7- benzyl-fapy-dg containing DNA”. X-ray diffraction, 1 ligand (2ON), 3 pockets (best druggability 0.71). MolNFT v1 #103331 on…
- PDB
- 4PDI
- Type
- protein + DNA
- Length
- 296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidine-DNA glycosylase; DNA (5'-D(*CP*TP*CP*TP*TP*TP*(SOS)P*TP*TP*TP*CP*TP*CP…
- EC
- 3.2.2.23
- UniProt
- P42371
- Ligands
- 2ON
- Pockets
- 3 · 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) | protein | 268 | 33% helix, 23% strand | P42371 |
| B | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(SOS)P*TP*TP*TP*CP*TP*CP*G)- 3') | dna | 14 | — | — |
| C | DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') | dna | 14 | — | — |
Ligands and binding sites
- 2ON · 2-sulfanyl-1,9-dihydro-6H-purin-6-one · ligand · chains 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 | 591 | 0.71 | 0.80 | 42 | empty |
| 2 | 294 | 0.55 | 0.76 | 41 | empty |
| 3 | 134 | 0.44 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 862 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 548 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–C · 428 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, nucleotide modification).
Compared structures
- 4PDI · Crystal structure of a complex between an inhibited LlFpg and a N7-Benzyl-Fapy-dG… · 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 0.99
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 4PDI · PDBe 4PDI · UniProt P42371
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