MolNFT v1 · #11187 · protein
Crystal structure of thermoactinomyces vulgaris R-47 alpha-amylase 2 mutant F286A
1JF5 · Alpha amylase II: “Crystal structure of thermoactinomyces vulgaris R-47 alpha-amylase 2 mutant F286A”. X-ray diffraction, 1 ligand (CA), 17 pockets (best druggability 0.90). MolNFT v1 #11187 on GenesisL1: 3D structure, binding sites…
- PDB
- 1JF5
- Type
- protein
- Length
- 1,170 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha amylase II
- EC
- 3.2.1.135
- UniProt
- Q08751
- Ligands
- CA
- Pockets
- 17 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha amylase II (EC 3.2.1.135) | protein | 585 | 30% helix, 25% strand | Q08751 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.90 | 0.92 | 129 | empty |
| 2 | 73 | 0.55 | 0.87 | 20 | empty |
| 3 | 201 | 0.54 | 0.79 | 28 | empty |
| 4 | 199 | 0.54 | 0.79 | 26 | empty |
| 5 | 221 | 0.50 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2328 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1JF5 · Crystal structure of thermoactinomyces vulgaris R-47 alpha-amylase 2 mutant F286A · the same entry in another collection · chain A against A, TM-score 1.00
- Q08751 · AlphaFold monomer V2.0 prediction for neopullulanase 2 (Q08751) · a predicted model of the same protein · 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 Q08751
- Elsewhere: RCSB PDB 1JF5 · PDBe 1JF5 · UniProt Q08751
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