MolNFT v1 · #168283 · protein
Acarbose kinase acbk as a complex with acarbose and AMP-pnp
6WB7 · Acarbose 7(IV)-phosphotransferase: “Acarbose kinase acbk as a complex with acarbose and AMP-pnp”. X-ray diffraction, 5 ligands (AC1, ANP, GLC), 11 pockets (best druggability 0.77). MolNFT v1 #168283 on GenesisL1: 3D structure…
- PDB
- 6WB7
- Type
- protein
- Length
- 1,176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acarbose 7(IV)-phosphotransferase
- EC
- 2.7.1.187
- UniProt
- Q8RMD4
- Ligands
- AC1, ANP, GLC, MN, NA
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acarbose 7(IV)-phosphotransferase (EC 2.7.1.187) | protein | 296 | 30% helix, 24% strand | Q8RMD4 |
| B, C | Acarbose 7(IV)-phosphotransferase (EC 2.7.1.187) | protein | 293 | 31% helix, 24% strand | Q8RMD4 |
| D | Acarbose 7(IV)-phosphotransferase (EC 2.7.1.187) | protein | 294 | 32% helix, 24% strand | Q8RMD4 |
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 · 4 copies · chains A, B, C, D
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.77 | 0.83 | 68 | GLC, AC1, ANP, MN |
| 2 | 640 | 0.77 | 0.83 | 71 | GLC, AC1, ANP, MN |
| 3 | 774 | 0.77 | 0.81 | 84 | GLC, AC1, ANP, MN |
| 4 | 688 | 0.77 | 0.82 | 71 | GLC, AC1, ANP, MN |
| 5 | 120 | 0.70 | 0.91 | 32 | NA |
Interfaces
2 interfaces between chains.
- A–B · 1583 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1533 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6WB7 · Acarbose Kinase AcbK as a Complex with Acarbose and AMP-PNP · the same entry in another collection · chain D against D, TM-score 1.00
- Q8RMD4 · AlphaFold monomer V2.0 prediction for acarbose 7(IV)-phosphotransferase (Q8RMD4) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q8RMD4
- Elsewhere: RCSB PDB 6WB7 · PDBe 6WB7 · UniProt Q8RMD4
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