MolNFT v1 · #136087 · protein
Crystal structure of an oxidoreductase from agrobacterium radiobacter in complex with NAD+, R-2,3-dihydroxyisovalerate and magnesium
5UIA · Oxidoreductase protein: “Crystal structure of an oxidoreductase from agrobacterium radiobacter in complex with NAD+…”. X-ray diffraction, 3 ligands (NAD, 89V, MG), 5 pockets (best druggability 0.73). MolNFT v1 #136087 on GenesisL1…
- PDB
- 5UIA
- 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, 89V, 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
- 89V · (2S)-2,3-dihydroxy-3-methylbutanoic acid · 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 | 537 | 0.73 | 0.81 | 41 | empty |
| 2 | 400 | 0.73 | 0.83 | 55 | NAD, 89V |
| 3 | 456 | 0.73 | 0.82 | 50 | NAD, 89V |
| 4 | 61 | 0.37 | 0.79 | 18 | empty |
| 5 | 54 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1439 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5UIA · 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 5UIA · PDBe 5UIA · UniProt B9JK80
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