Research workbench

Human pancreatic alpha-amylase complexed with nitrite

Analyse Human pancreatic alpha-amylase complexed with nitrite in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QMK
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: NAG, CA, NO2
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pancreatic alpha-amylase (EC 3.2.1.1)	protein	496	27% helix, 24% strand	P04746

Ligands and binding sites

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	228	0.55	0.78	22	empty
2	102	0.35	0.74	22	empty
3	56	0.31	0.76	13	empty
4	57	0.31	0.76	17	empty

Modifications

Observed in the structure: 5 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).

Compared structures

2QMK · Human pancreatic alpha-amylase complexed with nitrite · 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 2QMK · PDBe 2QMK · UniProt P04746

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