MolNFT v1 · #121477 · protein
Crystal structure of ketopantoate reductase from thermococcus kodakarensis complexed with NADP+
5HWS · 2-dehydropantoate 2-reductase: “Crystal structure of ketopantoate reductase from thermococcus kodakarensis complexed with NADP+”. X-ray diffraction, 1 ligand (NAP), 13 pockets (best druggability 0.76). MolNFT v1 #121477 on…
- PDB
- 5HWS
- Type
- protein
- Length
- 1,196 residues
- Chains
- 4
- 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
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 298 | 48% helix, 19% strand | Q5JGC2 |
| C | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 303 | 46% helix, 19% strand | Q5JGC2 |
| D | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 297 | 47% helix, 19% strand | Q5JGC2 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.76 | 0.80 | 54 | NAP |
| 2 | 892 | 0.75 | 0.79 | 66 | NAP |
| 3 | 739 | 0.75 | 0.80 | 59 | NAP |
| 4 | 707 | 0.75 | 0.80 | 61 | NAP |
| 5 | 68 | 0.45 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 993 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 976 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 433 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5HWS · Crystal structure of ketopantoate reductase from Thermococcus kodakarensis complexed with… · 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 C 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 Q5JGC2
- Elsewhere: RCSB PDB 5HWS · PDBe 5HWS · UniProt Q5JGC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.