Research workbench
Crystal structure of arabidopsis thaliana fpg
Analyse Crystal structure of arabidopsis thaliana fpg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TWM
- Type
- protein + DNA
- Length
- 584 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formamidopyrimidine-DNA glycosylase 1; 5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP…
- EC
- 3.2.2.23
- UniProt
- Q9SBB4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Formamidopyrimidine-DNA glycosylase 1 (EC 3.2.2.23) | protein | 261 | 30% helix, 26% strand | Q9SBB4 |
| C, E | 5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)- 3' | dna | 16 | — | — |
| D, F | 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3' | dna | 15 | — | — |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.69 | 0.79 | 42 | empty |
| 2 | 621 | 0.65 | 0.75 | 46 | empty |
| 3 | 615 | 0.65 | 0.75 | 46 | empty |
| 4 | 336 | 0.60 | 0.78 | 31 | empty |
| 5 | 61 | 0.56 | 0.89 | 15 | empty |
Interfaces
7 interfaces between chains.
- B–E · 629 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–F · 615 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- A–C · 599 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 590 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- A–D · 551 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3TWM · Crystal structure of Arabidopsis thaliana FPG · the same entry in another collection · 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 Q9SBB4
- Elsewhere: RCSB PDB 3TWM · PDBe 3TWM · UniProt Q9SBB4
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