Research workbench
Crystal structure of archaeal ketopantoate reductase complexed with coenzyme a and 2-oxopantoate
Analyse Crystal structure of archaeal ketopantoate reductase complexed with coenzyme a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AYV
- Type
- protein
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydropantoate 2-reductase
- EC
- 1.1.1.169
- UniProt
- Q5JGC2
- Ligands
- NAP, COA, KPL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 300 | 50% helix, 18% strand | Q5JGC2 |
| B | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 303 | 49% helix, 18% strand | Q5JGC2 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- COA · Coenzyme A · ligand · chains B
- KPL · Ketopantoate · ligand · chains B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.75 | 0.79 | 67 | NAP, ACT |
| 2 | 353 | 0.72 | 0.84 | 49 | COA, KPL |
| 3 | 84 | 0.36 | 0.76 | 16 | empty |
| 4 | 76 | 0.32 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1043 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5AYV · Crystal structure of archaeal ketopantoate reductase complexed with coenzyme A and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JGC2 · AlphaFold monomer V2.0 prediction for 2-dehydropantoate 2-reductase (Q5JGC2) · 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 Q5JGC2
- Elsewhere: RCSB PDB 5AYV · PDBe 5AYV · UniProt Q5JGC2
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