Research workbench
Microbiome-derived acarbose kinase MAK1 as a complex with acarbose and AMP-pnp
Analyse Microbiome-derived acarbose kinase MAK1 as a complex with acarbose and AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WB5
- Type
- protein
- Length
- 605 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acarbose kinase MAK1
- Ligands
- AC1, ANP, GLC, MN
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acarbose kinase MAK1 | protein | 299 | 35% helix, 27% strand | — |
| B | Acarbose kinase MAK1 | protein | 306 | 35% helix, 27% 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
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.80 | 0.83 | 76 | GLC, AC1, ANP, MN |
| 2 | 711 | 0.79 | 0.83 | 77 | GLC, AC1, ANP, MN |
| 3 | 70 | 0.43 | 0.81 | 19 | empty |
| 4 | 113 | 0.40 | 0.76 | 19 | empty |
| 5 | 63 | 0.32 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1281 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6WB5 · Microbiome-derived Acarbose Kinase Mak1 as a Complex with Acarbose and AMP-PNP · 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 6WB5 · PDBe 6WB5
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