MolNFT v1 · #82410 · protein

Structure of an alpha-amylase from malbranchea cinnamomea

3VM7: “Structure of an alpha-amylase from malbranchea cinnamomea”. X-ray diffraction, 3 ligands (NAG, GLC, CA), 2 pockets (best druggability 0.57). MolNFT v1 #82410 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VM7
Type: protein
Length: 470 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-amylase
Ligands: NAG, GLC, CA
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-amylase	protein	470	36% helix, 20% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
GLC · alpha-D-glucopyranose · sugar · chains A
CA · Calcium ion · metal · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

2 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	293	0.57	0.77	29	GLC
2	69	0.31	0.74	16	empty

Modifications

Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

3VM7 · Structure of an Alpha-Amylase from Malbranchea cinnamomea · 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
Elsewhere: RCSB PDB 3VM7 · PDBe 3VM7

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