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Functional characterization and crystal structure of thermostable amylase from thermotoga petrophila, reveals high thermostability and an archaic form of dimerization
Analyse Functional characterization and crystal structure of thermostable amylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M99
- Type
- protein
- Length
- 1,011 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase
- EC
- 3.2.1.1
- UniProt
- A0A059TXD8
- Ligands
- NA, K, CA
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase (EC 3.2.1.1) | protein | 506 | 33% helix, 22% strand | A0A059TXD8 |
| B | Alpha-amylase (EC 3.2.1.1) | protein | 505 | 33% helix, 21% strand | A0A059TXD8 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.87 | 0.87 | 88 | K, EDO |
| 2 | 150 | 0.47 | 0.78 | 22 | empty |
| 3 | 75 | 0.46 | 0.82 | 15 | empty |
| 4 | 106 | 0.46 | 0.79 | 17 | empty |
| 5 | 124 | 0.45 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1616 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5M99 · Functional Characterization and Crystal Structure of Thermostable Amylase from Thermotoga… · 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 A0A059TXD8
- Elsewhere: RCSB PDB 5M99 · PDBe 5M99 · UniProt A0A059TXD8
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