Research workbench
Structure of tenebrio molitor larval alpha-amylase in complex with ragi bifunctional inhibitor
Analyse Structure of tenebrio molitor larval alpha-amylase in complex with ragi… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TMQ
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (alpha-amylase); Protein (ragi bifunctional inhibitor)
- EC
- 3.2.1.1
- UniProt
- P56634, P01087
- Ligands
- CA, CL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (alpha-amylase) (EC 3.2.1.1) | protein | 471 | 28% helix, 25% strand | P56634 |
| B | Protein (ragi bifunctional inhibitor) | protein | 117 | 44% helix, 7% strand | P01087 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.63 | 0.84 | 38 | empty |
| 2 | 50 | 0.63 | 0.94 | 26 | empty |
| 3 | 141 | 0.43 | 0.76 | 28 | empty |
| 4 | 68 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1227 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 1TMQ · Structure of tenebrio molitor larval alpha-amylase in complex with ragi bifunctional… · the same entry in another collection · chain A against A, TM-score 1.00
- P56634 · AlphaFold monomer V2.0 prediction for alpha-amylase (P56634) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P01087 · AlphaFold monomer V2.0 prediction for alpha-AMYLASE/TRYPSIN inhibitor (P01087) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P56634
- Every structure of UniProt P01087
- Elsewhere: RCSB PDB 1TMQ · PDBe 1TMQ · UniProt P56634 · UniProt P01087
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