MolNFT v1 · #91655 · protein
Crystal structure of ureidoglycolate dehydrogenase in ternary complex with NADH and glyoxylate
4FJU: “Crystal structure of ureidoglycolate dehydrogenase in ternary complex with NADH and glyoxylate”. X-ray diffraction, 2 ligands (NAI, GLV), 6 pockets (best druggability 0.78). MolNFT v1 #91655 on GenesisL1: 3D structure, binding sites…
- PDB
- 4FJU
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ureidoglycolate dehydrogenase
- EC
- 1.1.1.154
- UniProt
- B1XGB5
- Ligands
- NAI, GLV
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ureidoglycolate dehydrogenase (EC 1.1.1.154) | protein | 338 | 43% helix, 18% strand | B1XGB5 |
| B | Ureidoglycolate dehydrogenase (EC 1.1.1.154) | protein | 312 | 42% helix, 20% strand | B1XGB5 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- GLV · Glyoxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.78 | 0.98 | 16 | empty |
| 2 | 512 | 0.73 | 0.81 | 67 | NAI |
| 3 | 566 | 0.71 | 0.80 | 68 | NAI, GLV |
| 4 | 78 | 0.33 | 0.74 | 20 | empty |
| 5 | 63 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3031 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4FJU · Crystal structure of ureidoglycolate dehydrogenase in ternary complex with NADH and… · 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 B1XGB5
- Elsewhere: RCSB PDB 4FJU · PDBe 4FJU · UniProt B1XGB5
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