Research workbench
Crystal structure of pseudomonas aeruginosa D-arginine dehydrogenase in complex with an (N5) flavin adduct
Analyse Crystal structure of pseudomonas aeruginosa D-arginine dehydrogenase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SM8
- Type
- protein
- Length
- 381 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent catabolic D-arginine dehydrogenase, daua
- EC
- 1.4.1.-
- UniProt
- Q9HXE3
- Ligands
- FNK
- Pockets
- 2 · best druggability 0.83
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 1.4.1.-) | protein | 381 | 30% helix, 27% strand | Q9HXE3 |
Ligands and binding sites
- FNK · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[7,8-dimethyl-5-(3-methylbutanoyl)-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate · ligand · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.83 | 0.90 | 76 | FNK |
| 2 | 61 | 0.33 | 0.76 | 14 | empty |
Compared structures
- 3SM8 · Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with an… · 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 0.98
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 3SM8 · PDBe 3SM8 · UniProt Q9HXE3
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