MolNFT v1 · #37786 · protein
Ternary crystal structure of human glyoxylate REDUCTASE/HYDROXYPYRUVATE reductase
2GCG: “Ternary crystal structure of human glyoxylate REDUCTASE/HYDROXYPYRUVATE reductase”. X-ray diffraction, 3 ligands (NDP, DGY, SO4), 15 pockets (best druggability 0.70). MolNFT v1 #37786 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2GCG
- Type
- protein
- Length
- 1,294 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyoxylate REDUCTASE/HYDROXYPYRUVATE reductase
- EC
- 1.1.1.79
- UniProt
- Q9UBQ7
- Ligands
- NDP, DGY, SO4
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glyoxylate REDUCTASE/HYDROXYPYRUVATE reductase (EC 1.1.1.79) | protein | 324 | 38% helix, 17% strand | Q9UBQ7 |
| B, D | Glyoxylate REDUCTASE/HYDROXYPYRUVATE reductase (EC 1.1.1.79) | protein | 323 | 37% helix, 17% strand | Q9UBQ7 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- DGY · (2R)-2,3-dihydroxypropanoic acid · ligand · 2 copies · chains A, B, C, D
- 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
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.70 | 0.82 | 50 | NDP, DGY |
| 2 | 397 | 0.70 | 0.82 | 44 | NDP |
| 3 | 389 | 0.69 | 0.81 | 46 | NDP |
| 4 | 420 | 0.69 | 0.80 | 48 | NDP, DGY |
| 5 | 211 | 0.60 | 0.81 | 34 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3267 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3188 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 120 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GCG · Ternary Crystal Structure of Human Glyoxylate Reductase/Hydroxypyruvate Reductase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBQ7 · AlphaFold monomer V2.0 prediction for glyoxylate REDUCTASE/HYDROXYPYRUVATE reductase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UBQ7
- Elsewhere: RCSB PDB 2GCG · PDBe 2GCG · UniProt Q9UBQ7
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