MolNFT v1 · #153970 · protein
The crystal structure of KAND2 in complex with NADH and 3"-deamino-3"- hydroxykanamycin B
6JW8 · Dehydrogenase: “The crystal structure of KAND2 in complex with NADH and 3"-deamino-3"- hydroxykanamycin B”. X-ray diffraction, 2 ligands (NAI, CK0), 6 pockets (best druggability 0.76). MolNFT v1 #153970 on GenesisL1: 3D structure…
- PDB
- 6JW8
- 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, CK0
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dehydrogenase | protein | 342 | 38% helix, 24% strand | Q6L737 |
| B | Dehydrogenase | protein | 341 | 38% helix, 24% strand | Q6L737 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- CK0 · (2S,3R,4S,5S,6R)-2-[(1S,2S,3R,4S,6R)-3-[(2R,3R,4R,5S, 6R)-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol · ligand · chains A
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 | 648 | 0.76 | 0.81 | 58 | NAI |
| 2 | 589 | 0.74 | 0.81 | 58 | NAI, CK0 |
| 3 | 196 | 0.43 | 0.73 | 30 | empty |
| 4 | 84 | 0.31 | 0.73 | 27 | empty |
| 5 | 72 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1647 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 6JW8 · The crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin B · the same entry in another collection · chain B against B, 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 6JW8 · PDBe 6JW8 · UniProt Q6L737
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