Research workbench
Structure of human deoxyhypusine hydroxylase in complex with glycerol
Analyse Structure of human deoxyhypusine hydroxylase in complex with glycerol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D4Z
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyhypusine hydroxylase
- EC
- 1.14.99.29
- UniProt
- Q9BU89
- Ligands
- FE, OH
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyhypusine hydroxylase (EC 1.14.99.29) | protein | 288 | 75% helix, 0% strand | Q9BU89 |
| B | Deoxyhypusine hydroxylase (EC 1.14.99.29) | protein | 290 | 74% helix, 0% strand | Q9BU89 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 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 | 749 | 0.71 | 0.78 | 84 | empty |
| 2 | 80 | 0.41 | 0.79 | 18 | empty |
| 3 | 85 | 0.32 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1350 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4D4Z · STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE in complex with glycerol · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BU89 · AlphaFold monomer V2.0 prediction for deoxyhypusine hydroxylase (Q9BU89) · 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 Q9BU89
- Elsewhere: RCSB PDB 4D4Z · PDBe 4D4Z · UniProt Q9BU89
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