Research workbench
Crystal structure of thermoactinomyces vulgaris R-47 amylase 2/GAMMA- cyclodextrin complex
Analyse Crystal structure of thermoactinomyces vulgaris R-47 amylase 2/GAMMA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VFU
- Type
- protein
- Length
- 1,170 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neopullulanase 2
- EC
- 3.2.1.135
- UniProt
- Q08751
- Ligands
- GLC, CA
- Pockets
- 15 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neopullulanase 2 (EC 3.2.1.135) | protein | 585 | 28% helix, 25% strand | Q08751 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 16 copies · chains A, B
- 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
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.90 | 0.93 | 122 | empty |
| 2 | 56 | 0.71 | 0.98 | 22 | empty |
| 3 | 147 | 0.65 | 0.87 | 31 | empty |
| 4 | 291 | 0.56 | 0.76 | 33 | GLC |
| 5 | 189 | 0.55 | 0.79 | 32 | GLC |
Interfaces
1 interface between chains.
- A–B · 2355 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 1VFU · Crystal structure of Thermoactinomyces vulgaris R-47 amylase 2/gamma-cyclodextrin complex · 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 1VFU · PDBe 1VFU · UniProt Q08751
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