MolNFT v1 · #171015 · protein

Taka-amylase

6YQ7 · Alpha-amylase: “Taka-amylase”. X-ray diffraction, 2 ligands (NAG, CA), 4 pockets (best druggability 0.61). MolNFT v1 #171015 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YQ7
Type: protein
Length: 952 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-amylase
EC: 3.2.1.1
UniProt: A0A1S9DH83
Ligands: NAG, CA
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alpha-amylase (EC 3.2.1.1)	protein	476	36% helix, 21% strand	A0A1S9DH83

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	331	0.61	0.78	29	empty
2	332	0.61	0.78	25	EDO
3	293	0.58	0.78	55	empty
4	328	0.55	0.75	49	empty

Interfaces

1 interface between chains.

A–B · 634 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6YQ7 · Taka-amylase · the same entry in another collection · 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 A0A1S9DH83
Elsewhere: RCSB PDB 6YQ7 · PDBe 6YQ7 · UniProt A0A1S9DH83

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