MolNFT v1 · #136913 · protein
Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase SMC04462 (smghrb) from sinorhizobium meliloti in complex with NADP and 2-keto-D-gluconic acid
5V7N: “Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase SMC04462 (smghrb) from…”. X-ray diffraction, 5 ligands (NAP, 8YV, MG), 8 pockets (best druggability 0.73). MolNFT v1 #136913 on GenesisL1: 3D structure…
- PDB
- 5V7N
- Type
- protein
- Length
- 1,273 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
- NAP, 8YV, MG, NA, CL
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 319 | 39% helix, 18% strand | Q92LZ4 |
| B, C, D | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 318 | 39% helix, 18% strand | Q92LZ4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 8YV · 2-keto-D-gluconic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains A
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 | 715 | 0.73 | 0.79 | 70 | NAP, 8YV, CL, MG |
| 2 | 740 | 0.73 | 0.79 | 72 | NAP, 8YV, CL |
| 3 | 696 | 0.72 | 0.79 | 73 | NAP, 8YV, CL, MG |
| 4 | 741 | 0.72 | 0.78 | 71 | NAP, 8YV, CL |
| 5 | 61 | 0.31 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2280 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2277 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5V7N · 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 5V7N · PDBe 5V7N · UniProt Q92LZ4
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