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The crystal structure of a complex between the llfpg protein, a thf- DNA and an inhibitor
Analyse The crystal structure of a complex between the llfpg protein, a thf- DNA and an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RP7
- Type
- protein + DNA
- Length
- 295 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, 4.2.99.18
- UniProt
- A0A165FVI1
- Ligands
- KD8
- Pockets
- 4 · 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, 4.2.99.18) | protein | 267 | 33% helix, 23% strand | A0A165FVI1 |
| 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 | — | — |
Ligands and binding sites
- KD8 · 6,7-dimethyl-2-sulfanylidene-1~{H}-pteridin-4-one · ligand · chains A, D
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.71 | 0.79 | 44 | KD8 |
| 2 | 227 | 0.55 | 0.78 | 29 | empty |
| 3 | 117 | 0.41 | 0.76 | 20 | GOL |
| 4 | 57 | 0.29 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–D · 692 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–E · 545 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–E · 431 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 6RP7 · The crystal structure of a complex between the LlFpg protein, a THF-DNA and an inhibitor · 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 A0A165FVI1
- Elsewhere: RCSB PDB 6RP7 · PDBe 6RP7 · UniProt A0A165FVI1
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