Research workbench
Crystal structure of glyoxylate reductase (PH0597) from pyrococcus horikoshii OT3, complexed with NADP (P61)
Analyse Crystal structure of glyoxylate reductase (PH0597) from pyrococcus horikoshii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DBZ
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyoxylate reductase
- EC
- 1.1.1.26
- UniProt
- O58320
- Ligands
- NAP, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyoxylate reductase (EC 1.1.1.26) | protein | 333 | 39% helix, 16% strand | O58320 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.72 | 0.84 | 47 | SO4, NAP |
| 2 | 343 | 0.70 | 0.83 | 49 | SO4, NAP |
| 3 | 192 | 0.52 | 0.78 | 25 | empty |
| 4 | 160 | 0.51 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3738 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 2DBZ · Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3… · the same entry in another collection · chain A against A, TM-score 1.00
- O58320 · AlphaFold monomer V2.0 prediction for glyoxylate reductase (O58320) · 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 O58320
- Elsewhere: RCSB PDB 2DBZ · PDBe 2DBZ · UniProt O58320
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.