Research workbench
Crystal structure of NADPH-dependent GLYOXYLATE/HYDROXYPYRUVATE reductase SMC04462 (smghrb) from sinorhizobium meliloti in complex with 2'-phospho-ADP-ribose
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
- 5J23
- Type
- protein
- Length
- 1,272 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-hydroxyacid dehydrogenase
- UniProt
- Q92LZ4
- Ligands
- A2R, CL
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-hydroxyacid dehydrogenase | protein | 318 | 38% helix, 17% strand | Q92LZ4 |
Ligands and binding sites
- A2R · [(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 7 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.73 | 0.78 | 68 | CL, A2R |
| 2 | 728 | 0.73 | 0.79 | 75 | CL, A2R |
| 3 | 716 | 0.72 | 0.78 | 72 | CL, A2R |
| 4 | 744 | 0.72 | 0.78 | 68 | CL, A2R |
| 5 | 66 | 0.32 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–D · 2316 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2298 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5J23 · 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 5J23 · PDBe 5J23 · UniProt Q92LZ4
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