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Crystal structure of alpha-amylase amyi-1 from oryza sativa

Analyse Crystal structure of alpha-amylase amyi-1 from oryza sativa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WN6
Type: protein
Length: 1,616 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-amylase
EC: 3.2.1.1
UniProt: P17654
Ligands: CA
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Alpha-amylase (EC 3.2.1.1)	protein	404	34% helix, 18% strand	P17654

Ligands and binding sites

CA · Calcium ion · metal · 12 copies · chains A, B, C, D
GOL · Glycerol · additive · 9 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, D, B, C
TAR · D(-)-tartaric acid · additive · 6 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1184	0.80	0.81	109	GOL
2	1067	0.77	0.79	74	GOL
3	419	0.69	0.81	37	PEG
4	251	0.63	0.81	41	empty
5	407	0.57	0.75	50	TAR

Interfaces

5 interfaces between chains.

C–D · 596 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 556 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 534 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 10 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 10 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3WN6 · Crystal structure of alpha-amylase AmyI-1 from Oryza sativa · the same entry in another collection · chain D against D, TM-score 1.00
P17654 · AlphaFold monomer V2.0 prediction for alpha-amylase (P17654) · a predicted model of the same protein · chain B 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 P17654
Elsewhere: RCSB PDB 3WN6 · PDBe 3WN6 · UniProt P17654

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