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Crystal structure of yeast acetyl-coenzyme a synthetase in complex with AMP

Analyse Crystal structure of yeast acetyl-coenzyme a synthetase in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RY2
Type: protein
Length: 615 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetyl-coenzyme a synthetase 1
EC: 6.2.1.1
UniProt: Q01574
Ligands: AMP
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetyl-coenzyme a synthetase 1 (EC 6.2.1.1)	protein	615	30% helix, 21% strand	Q01574

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	983	0.82	0.83	105	AMP
2	374	0.68	0.81	48	empty
3	53	0.34	0.78	16	empty
4	82	0.32	0.74	16	empty

Compared structures

1RY2 · Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP · the same entry in another collection · chain A against A, TM-score 1.00
Q01574 · AlphaFold monomer V2.0 prediction for acetyl-coenzyme a synthetase 1 (Q01574) · a predicted model of the same protein · chain A against A, TM-score 0.85

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 Q01574
Elsewhere: RCSB PDB 1RY2 · PDBe 1RY2 · UniProt Q01574

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