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Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase SMC04462 (smghrb) from sinorhizobium meliloti in complex with NADP and malonate
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
- 5V6Q
- Type
- protein
- Length
- 1,274 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, NA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 318 | 38% helix, 18% strand | Q92LZ4 |
| B | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 319 | 38% helix, 18% strand | Q92LZ4 |
| C | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 319 | 38% helix, 18% strand | Q92LZ4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B, D
- MLA · Malonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.73 | 0.79 | 71 | NAP, MLA |
| 2 | 750 | 0.72 | 0.78 | 65 | NAP, MLA |
| 3 | 704 | 0.72 | 0.78 | 69 | NAP, MLA |
| 4 | 715 | 0.71 | 0.78 | 69 | NAP, MLA |
| 5 | 68 | 0.32 | 0.75 | 20 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2294 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2293 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5V6Q · Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462… · the same entry in another collection · chain C against C, 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 5V6Q · PDBe 5V6Q · UniProt Q92LZ4
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