Research workbench
Crystal structure of the pig pancreatic-amylase complexed with R- nitrophenyl-a-D-maltoside
Analyse Crystal structure of the pig pancreatic-amylase complexed with R… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VAH
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase, pancreatic
- EC
- 3.2.1.1
- UniProt
- P00690
- Ligands
- NPO, CA, CL
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase, pancreatic (EC 3.2.1.1) | protein | 496 | 27% helix, 24% strand | P00690 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.59 | 0.78 | 30 | NPO |
| 2 | 86 | 0.41 | 0.78 | 19 | empty |
| 3 | 66 | 0.35 | 0.77 | 12 | empty |
| 4 | 70 | 0.31 | 0.75 | 21 | empty |
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1VAH · Crystal structure of the pig pancreatic-amylase complexed with r-nitrophenyl-a-D-maltoside · the same entry in another collection · chain A against A, TM-score 1.00
- P00690 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P00690) · 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 P00690
- Elsewhere: RCSB PDB 1VAH · PDBe 1VAH · UniProt P00690
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