MolNFT v1 · #27633 · protein

Crystal structure of staphylococcus aureus hmg-CoA synthase with hmg- CoA and acetoacetyl-CoA and acetylated cysteine

1XPM · 3-hydroxy-3-methylglutaryl CoA synthase: “Crystal structure of staphylococcus aureus hmg-CoA synthase with hmg- CoA and acetoacetyl-CoA and acetylated…”. X-ray diffraction, 3 ligands (HMG, CAA, SO4), 13 pockets (best druggability…

PDB: 1XPM
Type: protein
Length: 1,556 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-hydroxy-3-methylglutaryl CoA synthase
EC: 2.3.3.10
UniProt: Q79ZY6
Ligands: HMG, CAA, SO4
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	3-hydroxy-3-methylglutaryl CoA synthase (EC 2.3.3.10)	protein	389	40% helix, 25% strand	Q79ZY6

Ligands and binding sites

HMG · 3-hydroxy-3-methylglutaryl-coenzyme A · ligand · 4 copies · chains A, B, C, D
CAA · Acetoacetyl-coenzyme A · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1098	0.82	0.84	104	empty
2	752	0.81	0.84	79	empty
3	764	0.80	0.84	81	empty
4	150	0.66	0.86	22	HMG, CAA
5	159	0.64	0.85	22	HMG, CAA

Interfaces

5 interfaces between chains.

A–B · 2626 Å² buried · 50 hydrogen bonds · protein-protein
C–D · 2609 Å² buried · 49 hydrogen bonds · protein-protein
B–C · 370 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 243 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 218 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 modified (covalent ligand, acetylation).

Compared structures

1XPM · Crystal Structure of Staphylococcus aureus HMG-COA Synthase with HMG-CoA and… · 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 Q79ZY6
Elsewhere: RCSB PDB 1XPM · PDBe 1XPM · UniProt Q79ZY6

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