Research workbench
AMY2/BASI protein-protein complex from barley seed
Analyse AMY2/BASI protein-protein complex from barley seed in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AVA
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Barley alpha-amylase 2(CV menuet); Barley alpha-AMYLASE/SUBTILISIN inhibitor
- EC
- 3.2.1.1
- UniProt
- P04063, P07596
- Ligands
- CA
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Barley alpha-amylase 2(CV menuet) (EC 3.2.1.1) | protein | 403 | 33% helix, 20% strand | P04063 |
| C, D | Barley alpha-AMYLASE/SUBTILISIN inhibitor | protein | 181 | 3% helix, 40% strand | P07596 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.73 | 0.82 | 48 | CA |
| 2 | 521 | 0.71 | 0.80 | 45 | CA |
| 3 | 57 | 0.62 | 0.93 | 19 | empty |
| 4 | 399 | 0.57 | 0.75 | 46 | empty |
| 5 | 148 | 0.56 | 0.82 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1302 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1202 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 115 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1AVA · AMY2/BASI protein-protein complex from barley seed · the same entry in another collection · chain A against A, TM-score 1.00
- P04063 · AlphaFold monomer V2.0 prediction for alpha-amylase type B isozyme (P04063) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P07596 · AlphaFold monomer V2.0 prediction for alpha-AMYLASE/SUBTILISIN inhibitor (P07596) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P04063
- Every structure of UniProt P07596
- Elsewhere: RCSB PDB 1AVA · PDBe 1AVA · UniProt P04063 · UniProt P07596
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.