MolNFT v1 · #136895 · protein
Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase SMC04462 (smghrb) from sinorhizobium meliloti in complex with citrate
5V72: “Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase SMC04462 (smghrb) from…”. X-ray diffraction, 2 ligands (NA, CL), 10 pockets (best druggability 0.71). MolNFT v1 #136895 on GenesisL1: 3D structure, binding…
- PDB
- 5V72
- Type
- protein
- Length
- 1,264 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
- NA, CL
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 318 | 37% helix, 18% strand | Q92LZ4 |
| B | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 313 | 39% helix, 18% strand | Q92LZ4 |
| C | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 320 | 38% helix, 18% strand | Q92LZ4 |
| D | NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase (EC 1.1.1.81) | protein | 313 | 39% helix, 19% strand | Q92LZ4 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · chains A
- CIT · Citric acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.71 | 0.75 | 81 | empty |
| 2 | 626 | 0.68 | 0.77 | 63 | NA, CIT, CL |
| 3 | 573 | 0.67 | 0.77 | 53 | CL |
| 4 | 540 | 0.65 | 0.76 | 50 | CL |
| 5 | 416 | 0.63 | 0.77 | 44 | CL, GOL |
Interfaces
5 interfaces between chains.
- B–D · 2346 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2322 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 373 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 357 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5V72 · 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 5V72 · PDBe 5V72 · UniProt Q92LZ4
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