MolNFT v1 · #111770 · protein
Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase SMC02828 (smghra) from sinorhizobium meliloti in complex with NADPH and oxalate
4Z0P · NAD-dependent dehydrogenase: “Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase SMC02828 (smghra) from…”. X-ray diffraction, 3 ligands (OXD, NDP, CL), 2 pockets (best druggability 0.75). MolNFT v1 #111770 on…
- PDB
- 4Z0P
- Type
- protein
- Length
- 316 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent dehydrogenase
- EC
- 1.1.1.79
- UniProt
- Q92T34
- Ligands
- OXD, NDP, CL
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent dehydrogenase (EC 1.1.1.79) | protein | 316 | 35% helix, 16% strand | Q92T34 |
Ligands and binding sites
- OXD · Oxalic acid · ligand · 2 copies · chains A
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.75 | 0.82 | 71 | OXD, NDP |
| 2 | 89 | 0.44 | 0.80 | 16 | GOL |
Compared structures
- 4Z0P · Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828… · 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 Q92T34
- Elsewhere: RCSB PDB 4Z0P · PDBe 4Z0P · UniProt Q92T34
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