Research workbench
Thermoactinomyces vulgaris R-47 alpha-amylase I (tva I) mutant A357V/Q359N/Y360E (AQY/VNE)
Analyse Thermoactinomyces vulgaris R-47 alpha-amylase I (tva I) mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z0T
- Type
- protein
- Length
- 1,274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neopullulanase 1
- EC
- 3.2.1.135
- UniProt
- Q60053
- Ligands
- CA
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neopullulanase 1 (EC 3.2.1.135) | protein | 637 | 25% helix, 26% strand | Q60053 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.68 | 0.84 | 40 | empty |
| 2 | 254 | 0.68 | 0.84 | 39 | empty |
| 3 | 239 | 0.53 | 0.76 | 37 | MPD |
| 4 | 238 | 0.52 | 0.76 | 33 | MPD |
| 5 | 117 | 0.47 | 0.79 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 435 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5Z0T · Thermoactinomyces vulgaris R-47 alpha-amylase I (TVA I) mutant A357V/Q359N/Y360E (AQY/VNE) · the same entry in another collection · chain A against A, TM-score 1.00
- Q60053 · AlphaFold monomer V2.0 prediction for neopullulanase 1 (Q60053) · 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 Q60053
- Elsewhere: RCSB PDB 5Z0T · PDBe 5Z0T · UniProt Q60053
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