MolNFT v1 · #153969 · protein
The crystal structure of KAND2 in complex with NADH and 3"-deamino-3"- hydroxykanamycin a
6JW7 · Dehydrogenase: “The crystal structure of KAND2 in complex with NADH and 3"-deamino-3"- hydroxykanamycin a”. X-ray diffraction, 2 ligands (NAI, CJX), 7 pockets (best druggability 0.76). MolNFT v1 #153969 on GenesisL1: 3D structure…
- PDB
- 6JW7
- Type
- protein
- Length
- 683 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehydrogenase
- UniProt
- Q6L737
- Ligands
- NAI, CJX
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dehydrogenase | protein | 342 | 39% helix, 24% strand | Q6L737 |
| B | Dehydrogenase | protein | 341 | 39% helix, 24% strand | Q6L737 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- CJX · (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4, 6-bis(azanyl)-3-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3, 4,5-tris(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-oxane-3,4,5-triol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.76 | 0.83 | 57 | NAI, CJX |
| 2 | 558 | 0.73 | 0.81 | 51 | NAI |
| 3 | 81 | 0.49 | 0.83 | 20 | empty |
| 4 | 52 | 0.35 | 0.79 | 23 | empty |
| 5 | 78 | 0.31 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1665 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6JW7 · The crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin A · 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 Q6L737
- Elsewhere: RCSB PDB 6JW7 · PDBe 6JW7 · UniProt Q6L737
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