MolNFT v1 · #146326 · protein
2.1 a resolution structure of histamine dehydrogenase from rhizobium sp. 4-9
6DE6: “2.1 a resolution structure of histamine dehydrogenase from rhizobium sp. 4-9”. X-ray diffraction, 4 ligands (ADP, FMN, SF4), 13 pockets (best druggability 0.86). MolNFT v1 #146326 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DE6
- Type
- protein
- Length
- 1,341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histamine dehydrogenase
- UniProt
- Q60I59
- Ligands
- ADP, FMN, SF4, PO4
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histamine dehydrogenase | protein | 689 | 35% helix, 18% strand | Q60I59 |
| B | Histamine dehydrogenase | protein | 652 | 36% helix, 19% strand | Q60I59 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.86 | 0.89 | 97 | FMN |
| 2 | 192 | 0.78 | 0.93 | 48 | empty |
| 3 | 793 | 0.73 | 0.78 | 74 | empty |
| 4 | 614 | 0.72 | 0.80 | 52 | empty |
| 5 | 254 | 0.65 | 0.83 | 39 | ADP |
Interfaces
1 interface between chains.
- A–B · 4546 Ų buried · 71 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 6DE6 · 2.1 A resolution structure of histamine dehydrogenase from Rhizobium sp. 4-9 · 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 Q60I59
- Elsewhere: RCSB PDB 6DE6 · PDBe 6DE6 · UniProt Q60I59
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