MolNFT v1 · #66653 · protein
Crystal structure of PANE/APBA family ketopantoate reductase (YP_299159.1) from ralstonia eutropha JMP134 at 2.15 a resolution
3HWR · 2-dehydropantoate 2-reductase: “Crystal structure of PANE/APBA family ketopantoate reductase (YP_299159.1) from ralstonia eutropha JMP134 at…”. X-ray diffraction, 2 ligands (NDP, BCN), 6 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 3HWR
- Type
- protein
- Length
- 597 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
- Q46RB9
- Ligands
- NDP, BCN
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 299 | 49% helix, 20% strand | Q46RB9 |
| B | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 298 | 50% helix, 20% strand | Q46RB9 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- BCN · Bicine · ligand · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.73 | 0.78 | 61 | NDP, BCN, MRD |
| 2 | 767 | 0.72 | 0.78 | 63 | NDP, BCN, MRD |
| 3 | 86 | 0.43 | 0.79 | 22 | empty |
| 4 | 67 | 0.39 | 0.79 | 20 | empty |
| 5 | 103 | 0.36 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1263 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3HWR · Crystal structure of PanE/ApbA family ketopantoate reductase (YP_299159.1) from Ralstonia… · 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 Q46RB9
- Elsewhere: RCSB PDB 3HWR · PDBe 3HWR · UniProt Q46RB9
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