MolNFT v1 · #34305 · protein
Crystal structure of glyoxylate reductase (PH0597) from pyrococcus horikoshii OT3, complexed with NADP (P61)
2DBZ: “Crystal structure of glyoxylate reductase (PH0597) from pyrococcus horikoshii OT3, complexed with NADP (P61)”. X-ray diffraction, 2 ligands (NAP, SO4), 4 pockets (best druggability 0.72). MolNFT v1 #34305 on GenesisL1: 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
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