MolNFT v1 · #49668 · protein
Human pancreatic alpha-amylase complexed with nitrite and acarbose
2QV4: “Human pancreatic alpha-amylase complexed with nitrite and acarbose”. X-ray diffraction, 4 ligands (QV4, NAG, CA), 4 pockets (best druggability 0.57). MolNFT v1 #49668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2QV4
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic alpha-amylase
- EC
- 3.2.1.1
- UniProt
- P04746
- Ligands
- QV4, NAG, CA, NO2
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pancreatic alpha-amylase (EC 3.2.1.1) | protein | 496 | 29% helix, 24% strand | P04746 |
Ligands and binding sites
- QV4 · 4,6-dideoxy-4-{[(1S,4R,5R,6S)-4-{[alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl]oxy}-5,6-dihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- NO2 · Nitrite 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 | 222 | 0.57 | 0.79 | 26 | QV4 |
| 2 | 55 | 0.35 | 0.78 | 18 | empty |
| 3 | 52 | 0.34 | 0.78 | 14 | empty |
| 4 | 70 | 0.31 | 0.75 | 23 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 2QV4 · Human pancreatic alpha-amylase complexed with nitrite and acarbose · 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 2QV4 · PDBe 2QV4 · UniProt P04746
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