Research workbench
Human pancreatic alpha amylase in complex with peptide inhibitor piha- L5(D10Y)
Analyse Human pancreatic alpha amylase in complex with peptide inhibitor piha- L5(D10Y) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VA9
- Type
- protein
- Length
- 1,028 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic alpha-amylase; Peptide inhibitor piha-L5(D10Y)
- EC
- 3.2.1.1
- UniProt
- P04746
- Ligands
- ACE, CA, NH2, CL
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pancreatic alpha-amylase (EC 3.2.1.1) | protein | 496 | 28% helix, 23% strand | P04746 |
| C, D | Peptide inhibitor piha-L5(D10Y) | protein | 18 | 50% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains C, D
- CA · Calcium ion · metal · 2 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
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 | 823 | 0.74 | 0.79 | 89 | empty |
| 2 | 133 | 0.44 | 0.76 | 30 | empty |
| 3 | 112 | 0.42 | 0.77 | 20 | empty |
| 4 | 150 | 0.42 | 0.74 | 22 | empty |
| 5 | 118 | 0.41 | 0.76 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–D · 889 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 867 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 721 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 140 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 108 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 covalent, 2 modified (disulfide, covalent ligand, cyclization).
Compared structures
- 5VA9 · Human pancreatic alpha amylase in complex with peptide inhibitor piHA-L5(d10Y) · the same entry in another collection · chain A against A, TM-score 1.00
- P04746 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P04746) · 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 P04746
- Elsewhere: RCSB PDB 5VA9 · PDBe 5VA9 · UniProt P04746
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