Research workbench
TYR258PHE mutant of nikd, an unusual amino acid oxidase essential for nikkomycin biosynthesis: open form at 1.55A resolution
Analyse TYR258PHE mutant of nikd, an unusual amino acid oxidase essential for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HZL
- Type
- protein
- Length
- 394 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nikd protein
- UniProt
- Q9X9P9
- Ligands
- FAD, 6PC
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nikd protein | protein | 394 | 29% helix, 29% strand | Q9X9P9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- 6PC · Pyridine-2-carboxylic acid · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.85 | 0.87 | 105 | FAD, 6PC, MPD |
| 2 | 71 | 0.64 | 0.92 | 25 | empty |
| 3 | 58 | 0.39 | 0.80 | 13 | MPD |
| 4 | 50 | 0.31 | 0.77 | 13 | empty |
| 5 | 60 | 0.26 | 0.72 | 15 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 3HZL · Tyr258Phe mutant of NikD, an unusual amino acid oxidase essential for nikkomycin… · 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 Q9X9P9
- Elsewhere: RCSB PDB 3HZL · PDBe 3HZL · UniProt Q9X9P9
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