MolNFT v1 · #59037 · protein
Role of aromatic residues in starch binding
3BLK · Alpha-amylase 1: “Role of aromatic residues in starch binding”. X-ray diffraction, 5 ligands (AGL, HMC, GLC), 5 pockets (best druggability 0.58). MolNFT v1 #59037 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BLK
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase 1
- EC
- 3.2.1.1
- UniProt
- P04745
- Ligands
- AGL, HMC, GLC, CA, CL
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase 1 (EC 3.2.1.1) | protein | 496 | 27% helix, 24% strand | P04745 |
Ligands and binding sites
- AGL · 4-amino-4,6-dideoxy-alpha-D-glucopyranose · ligand · 2 copies · chains A
- HMC · 5-hydroxymethyl-chonduritol · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.58 | 0.78 | 26 | GLC, AGL, HMC |
| 2 | 72 | 0.34 | 0.76 | 15 | empty |
| 3 | 82 | 0.33 | 0.75 | 19 | empty |
| 4 | 72 | 0.32 | 0.74 | 17 | empty |
| 5 | 50 | 0.29 | 0.76 | 12 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 3BLK · Role of aromatic residues in starch binding · 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 P04745
- Elsewhere: RCSB PDB 3BLK · PDBe 3BLK · UniProt P04745
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