Research workbench
Histamine dehydrogenase from nocardiodes simplex
Analyse Histamine dehydrogenase from nocardiodes simplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K30
- Type
- protein
- Length
- 1,368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histamine dehydrogenase
- UniProt
- Q6IWJ5
- Ligands
- SF4, FMN, ADP
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Histamine dehydrogenase | protein | 684 | 35% helix, 19% strand | Q6IWJ5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.88 | 0.93 | 122 | FMN |
| 2 | 180 | 0.80 | 0.95 | 49 | empty |
| 3 | 727 | 0.77 | 0.81 | 89 | empty |
| 4 | 665 | 0.75 | 0.81 | 77 | empty |
| 5 | 62 | 0.73 | 0.98 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 4731 Ų buried · 79 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 3K30 · Histamine dehydrogenase from Nocardiodes simplex · 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 Q6IWJ5
- Elsewhere: RCSB PDB 3K30 · PDBe 3K30 · UniProt Q6IWJ5
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