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Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase SMC04462 (smghrb) from sinorhizobium meliloti in apo form
Analyse Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UOG
- Type
- protein
- Length
- 1,271 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase
- EC
- 1.1.1.81
- UniProt
- Q92LZ4
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 317 | 38% helix, 19% strand | Q92LZ4 |
| B | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 316 | 38% helix, 19% strand | Q92LZ4 |
| D | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 321 | 37% helix, 18% strand | Q92LZ4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.71 | 0.76 | 73 | SO4 |
| 2 | 674 | 0.70 | 0.77 | 56 | empty |
| 3 | 692 | 0.69 | 0.76 | 61 | empty |
| 4 | 628 | 0.66 | 0.76 | 62 | empty |
| 5 | 134 | 0.49 | 0.79 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2336 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2260 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5UOG · Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462… · 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 Q92LZ4
- Elsewhere: RCSB PDB 5UOG · PDBe 5UOG · UniProt Q92LZ4
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