Research workbench
Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH
Analyse Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H8A
- 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
- P77555
- Ligands
- NAI
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ureidoglycolate dehydrogenase (EC 1.1.1.154) | protein | 337 | 43% helix, 18% strand | P77555 |
| B | Ureidoglycolate dehydrogenase (EC 1.1.1.154) | protein | 313 | 40% helix, 18% strand | P77555 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
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 | 539 | 0.71 | 0.80 | 64 | NAI |
| 3 | 533 | 0.71 | 0.80 | 65 | NAI |
| 4 | 71 | 0.33 | 0.75 | 18 | empty |
| 5 | 59 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3076 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4H8A · Crystal structure of ureidoglycolate dehydrogenase in binary complex with NADH · the same entry in another collection · chain B against B, TM-score 1.00
- P77555 · AlphaFold monomer V2.0 prediction for ureidoglycolate dehydrogenase (NAD(+)) (P77555) · a predicted model of the same protein · 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 P77555
- Elsewhere: RCSB PDB 4H8A · PDBe 4H8A · UniProt P77555
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