MolNFT v1 · #126653 · protein
Functional characterization and crystal structure of thermostable amylase from thermotoga petrophila, reveals high thermostability and an archaic form of dimerization
5M99 · Alpha-amylase: “Functional characterization and crystal structure of thermostable amylase from thermotoga petrophila, reveals…”. X-ray diffraction, 3 ligands (NA, K, CA), 12 pockets (best druggability 0.87). MolNFT v1 #126653 on…
- 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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