Research workbench
Crystal structure of pseudomonas aeruginosa D-arginine dehydrogenase Y249F variant with FAD - yellow fraction
Analyse Crystal structure of pseudomonas aeruginosa D-arginine dehydrogenase Y249F… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P9D
- Type
- protein
- Length
- 375 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent catabolic D-arginine dehydrogenase daua
- EC
- 1.4.99.6
- UniProt
- Q9HXE3
- Ligands
- FDA
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-dependent catabolic D-arginine dehydrogenase daua (EC 1.4.99.6) | protein | 375 | 30% helix, 27% strand | Q9HXE3 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · chains A
- GOL · Glycerol · additive · 4 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.84 | 0.91 | 79 | FDA |
| 2 | 120 | 0.36 | 0.73 | 23 | GOL |
| 3 | 65 | 0.32 | 0.75 | 15 | empty |
Compared structures
- 6P9D · Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F variant with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HXE3 · AlphaFold monomer V2.0 prediction for FAD-dependent catabolic D-arginine dehydrogenase… · a predicted model of the same protein · 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 Q9HXE3
- Elsewhere: RCSB PDB 6P9D · PDBe 6P9D · UniProt Q9HXE3
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