Research workbench
Crystal structure of anubix (PADA1) in complex with FMN and dimethylallyl pyrophosphate
Analyse Crystal structure of anubix (PADA1) in complex with FMN and dimethylallyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QLG
- Type
- protein
- Length
- 1,123 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin prenyltransferase PAD1, mitochondrial
- EC
- 2.5.1.129
- UniProt
- A3F715
- Ligands
- DMA, FMN, PO4
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, D, E, F | Flavin prenyltransferase PAD1, mitochondrial (EC 2.5.1.129) | protein | 187 | 43% helix, 16% strand | A3F715 |
| A | Flavin prenyltransferase PAD1, mitochondrial (EC 2.5.1.129) | protein | 188 | 43% helix, 16% strand | A3F715 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 6 copies · chains C, A, E, B, D, F
- FMN · Flavin mononucleotide · ligand · 6 copies · chains C, A, B, E, D, F
- PO4 · Phosphate ion · ion · chains C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.87 | 0.87 | 118 | DMA, FMN |
| 2 | 390 | 0.82 | 0.90 | 47 | FMN, DMA |
| 3 | 687 | 0.73 | 0.80 | 57 | empty |
| 4 | 56 | 0.72 | 0.98 | 18 | PEG |
| 5 | 62 | 0.71 | 0.97 | 18 | PEG |
Interfaces
10 interfaces between chains.
- C–A · 1922 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1916 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 731 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 731 Ų buried · 12 hydrogen bonds · protein-protein
- C–B · 731 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6QLG · Crystal structure of AnUbiX (PadA1) in complex with FMN and dimethylallyl pyrophosphate · the same entry in another collection · chain C against C, 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 A3F715
- Elsewhere: RCSB PDB 6QLG · PDBe 6QLG · UniProt A3F715
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