MolNFT v1 · #34297 · protein
Crystal structure of glyoxylate reductase (PH0597) from pyrococcus horikoshii OT3, complexed with NADP (P1)
2DBR: “Crystal structure of glyoxylate reductase (PH0597) from pyrococcus horikoshii OT3, complexed with NADP (P1)”. X-ray diffraction, 2 ligands (NAP, SO4), 11 pockets (best druggability 0.82). MolNFT v1 #34297 on GenesisL1: 3D structure…
- PDB
- 2DBR
- Type
- protein
- Length
- 1,998 residues
- Chains
- 6
- 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
- 11 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glyoxylate reductase (EC 1.1.1.26) | protein | 333 | 39% helix, 17% strand | O58320 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, C, B, D, E, F
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.82 | 0.85 | 85 | SO4, NAP |
| 2 | 782 | 0.76 | 0.80 | 70 | empty |
| 3 | 790 | 0.74 | 0.79 | 85 | SO4, NAP |
| 4 | 263 | 0.74 | 0.88 | 45 | SO4, NAP |
| 5 | 268 | 0.73 | 0.87 | 46 | SO4, NAP |
Interfaces
8 interfaces between chains.
- C–D · 3759 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 3725 Ų buried · 55 hydrogen bonds · protein-protein
- E–F · 3703 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 619 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 478 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2DBR · Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3… · the same entry in another collection · chain F against F, 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 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 O58320
- Elsewhere: RCSB PDB 2DBR · PDBe 2DBR · UniProt O58320
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