Research workbench
Microbiome-derived acarbose kinase MAK1 labeled with selenomethionine
Analyse Microbiome-derived acarbose kinase MAK1 labeled with selenomethionine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WB4
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acarbose kinase MAK1
- Ligands
- AC1, ATP, GLC, CA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acarbose kinase MAK1 | protein | 298 | 35% helix, 24% strand | — |
| B | Acarbose kinase MAK1 | protein | 306 | 34% helix, 24% strand | — |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.78 | 0.81 | 77 | GLC, AC1, ATP, CA |
| 2 | 793 | 0.73 | 0.78 | 68 | GLC, AC1, ATP, CA |
| 3 | 87 | 0.59 | 0.88 | 24 | empty |
| 4 | 137 | 0.44 | 0.76 | 21 | empty |
| 5 | 98 | 0.42 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1163 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 6WB4 · Microbiome-derived Acarbose Kinase Mak1 Labeled with selenomethionine · 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
- Elsewhere: RCSB PDB 6WB4 · PDBe 6WB4
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