Research workbench
Crystal structure of the ketone reductase ChKRED20 from the genome of Chryseobacterium sp. CA49 complexed with NAD
Analyse Crystal structure of the ketone reductase ChKRED20 from the genome of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IXM
- Type
- protein
- Length
- 982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.601
- Source
- Chryseobacterium sp. CA49
- Molecule
- Short-chain dehydrogenase reductase
- UniProt
- X2D0L0
- Ligands
- NAD
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · resolution 1.601 · 2 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Short-chain dehydrogenase reductase | protein | 248 | 51% helix, 17% strand | X2D0L0 |
| B | Short-chain dehydrogenase reductase | protein | 238 | 49% helix, 18% strand | X2D0L0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.86 | 0.89 | 57 | empty |
| 2 | 1045 | 0.80 | 0.81 | 101 | NAD |
| 3 | 755 | 0.73 | 0.78 | 69 | NAD |
| 4 | 272 | 0.55 | 0.76 | 35 | NAD |
| 5 | 119 | 0.45 | 0.78 | 24 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1597 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1587 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1382 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1380 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 247 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6IXM · Crystal structure of the ketone reductase CHKRED20 from the genome of chryseobacterium… · 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 X2D0L0
- Elsewhere: RCSB PDB 6IXM · PDBe 6IXM · UniProt X2D0L0
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