MolNFT v1 · #144076 · protein
Crystal structure of pyrococcus yayanosii glyoxylate hydroxypyruvate reductase in complex with NADP and malonate (re-refinement of 5AOW)
6BII · Glyoxylate reductase: “Crystal structure of pyrococcus yayanosii glyoxylate hydroxypyruvate reductase in complex with NADP and…”. X-ray diffraction, 1 ligand (NAP), 5 pockets (best druggability 0.70). MolNFT v1 #144076 on GenesisL1…
- PDB
- 6BII
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyoxylate reductase
- EC
- 1.1.1.26
- UniProt
- F8AEA4
- Ligands
- NAP
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyoxylate reductase (EC 1.1.1.26) | protein | 332 | 40% helix, 16% strand | F8AEA4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- MLI · Malonate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.70 | 0.83 | 46 | NAP, MLI |
| 2 | 317 | 0.70 | 0.84 | 43 | NAP, MLI, GOL |
| 3 | 177 | 0.49 | 0.77 | 19 | empty |
| 4 | 181 | 0.49 | 0.77 | 25 | empty |
| 5 | 74 | 0.42 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3559 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 6BII · Crystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruvate Reductase in complex… · 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 F8AEA4
- Elsewhere: RCSB PDB 6BII · PDBe 6BII · UniProt F8AEA4
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