MolNFT v1 · #103329 · protein + DNA
Crystal structure of a complex between an inhibited llfpg and a thf containing DNA
4PDG · Formamidopyrimidine-DNA glycosylase: “Crystal structure of a complex between an inhibited llfpg and a thf containing DNA”. X-ray diffraction, 1 ligand (2ON), 3 pockets (best druggability 0.70). MolNFT v1 #103329 on GenesisL1: 3D…
- PDB
- 4PDG
- Type
- protein + DNA
- Length
- 294 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*(3DR)P*TP*TP*TP*CP*TP*CP…
- EC
- 3.2.2.23
- UniProt
- P42371
- Ligands
- 2ON
- Pockets
- 3 · best druggability 0.70
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 | 266 | 33% helix, 23% strand | P42371 |
| B | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)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
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.70 | 0.81 | 42 | empty |
| 2 | 223 | 0.50 | 0.75 | 26 | empty |
| 3 | 125 | 0.39 | 0.75 | 20 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 696 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 546 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–C · 534 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, nucleotide modification).
Compared structures
- 4PDG · Crystal structure of a complex between an inhibited LlFpg and a THF containing DNA · 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 4PDG · PDBe 4PDG · UniProt P42371
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