MolNFT v1 · #152915 · protein
Crystal structure of the ketone reductase CHKRED20 from the genome of chryseobacterium sp. CA49 complexed with NAD
6IXM · Short-chain dehydrogenase reductase: “Crystal structure of the ketone reductase CHKRED20 from the genome of chryseobacterium sp. CA49 complexed…”. X-ray diffraction, 1 ligand (NAD), 10 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 6IXM
- Type
- protein
- Length
- 982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain dehydrogenase reductase
- UniProt
- X2D0L0
- Ligands
- NAD
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 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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