Research workbench
CPF_2247, a novel alpha-amylase from clostridium perfringens
Analyse CPF_2247, a novel alpha-amylase from clostridium perfringens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3REN
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase, family 8
- UniProt
- Q0TNX0
- Ligands
- MG, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase, family 8 | protein | 337 | 50% helix, 13% strand | Q0TNX0 |
| B | Glycosyl hydrolase, family 8 | protein | 332 | 50% helix, 13% strand | Q0TNX0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.78 | 0.84 | 55 | EDO |
| 2 | 261 | 0.74 | 0.87 | 31 | empty |
| 3 | 490 | 0.61 | 0.75 | 59 | empty |
| 4 | 269 | 0.53 | 0.75 | 34 | MG |
| 5 | 105 | 0.36 | 0.73 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1043 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3REN · CPF_2247, a novel alpha-amylase from Clostridium perfringens · 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 Q0TNX0
- Elsewhere: RCSB PDB 3REN · PDBe 3REN · UniProt Q0TNX0
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