Research workbench
Crystal structure of an oxidoreductase from agrobacterium radiobacter in complex with NAD+, D-apionate and magnesium
Analyse Crystal structure of an oxidoreductase from agrobacterium radiobacter in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UHZ
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase protein
- UniProt
- B9JK80
- Ligands
- NAD, 89Y, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxidoreductase protein | protein | 342 | 39% helix, 25% strand | B9JK80 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 89Y · (3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.73 | 0.81 | 41 | empty |
| 2 | 382 | 0.73 | 0.83 | 50 | NAD, 89Y |
| 3 | 410 | 0.72 | 0.83 | 55 | NAD, 89Y |
| 4 | 57 | 0.40 | 0.81 | 16 | empty |
| 5 | 53 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1430 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5UHZ · Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- B9JK80 · AlphaFold monomer V2.0 prediction for D-apiose dehydrogenase (B9JK80) · a predicted model of the same protein · chain B 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 B9JK80
- Elsewhere: RCSB PDB 5UHZ · PDBe 5UHZ · UniProt B9JK80
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