MolNFT v1 · #153640 · protein
Crystal structure of sulfoacetaldehyde reductase from bifidobacterium kashiwanohense in complex with NAD+
6JKP · Methanol dehydrogenase: “Crystal structure of sulfoacetaldehyde reductase from bifidobacterium kashiwanohense in complex with NAD+”. X-ray diffraction, 2 ligands (NAD, ZN), 12 pockets (best druggability 0.75). MolNFT v1 #153640 on…
- PDB
- 6JKP
- Type
- protein
- Length
- 1,504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methanol dehydrogenase
- UniProt
- A0A0A7I0A5
- Ligands
- NAD, ZN
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Methanol dehydrogenase | protein | 376 | 54% helix, 10% strand | A0A0A7I0A5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.75 | 0.82 | 58 | NAD |
| 2 | 538 | 0.75 | 0.82 | 56 | NAD |
| 3 | 541 | 0.74 | 0.82 | 52 | NAD |
| 4 | 726 | 0.69 | 0.76 | 58 | NAD, ZN |
| 5 | 381 | 0.67 | 0.81 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–B · 630 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 342 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 208 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 135 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6JKP · Crystal structure of sulfoacetaldehyde reductase from Bifidobacterium kashiwanohense in… · 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 A0A0A7I0A5
- Elsewhere: RCSB PDB 6JKP · PDBe 6JKP · UniProt A0A0A7I0A5
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