MolNFT v1 · #161377 · protein

Citryl-CoA lyase core module of chlorobium limicola ATP citrate lyase in complex with acetyl-CoA and L-malate

6QCL · ATP-citrate lyase alpha-subunit: “Citryl-CoA lyase core module of chlorobium limicola ATP citrate lyase in complex with acetyl-CoA and L-malate”. X-ray diffraction, 3 ligands (LMR, ACO, CA), 20 pockets (best druggability 0.71).…

PDB: 6QCL
Type: protein
Length: 2,010 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-citrate lyase alpha-subunit
UniProt: Q9AJC4
Ligands: LMR, ACO, CA
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 56% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-citrate lyase alpha-subunit	protein	215	57% helix, 7% strand	Q9AJC4
B	ATP-citrate lyase alpha-subunit	protein	239	56% helix, 7% strand	Q9AJC4
C, D, G, H	ATP-citrate lyase alpha-subunit	protein	261	55% helix, 7% strand	Q9AJC4
E, F	ATP-citrate lyase alpha-subunit	protein	256	56% helix, 6% strand	Q9AJC4

Ligands and binding sites

LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains A, E, B, F, C, G, D, H
ACO · Acetyl coenzyme *A · ligand · 4 copies · chains A, E, B, F, C, G, D, H
CA · Calcium ion · metal · 2 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 2 copies · chains E, F, G, H, D
PGE · Triethylene glycol · additive · 2 copies · chains G, H

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	734	0.71	0.78	73	PG4
2	608	0.70	0.79	70	LMR, ACO
3	566	0.70	0.79	72	LMR, ACO
4	304	0.68	0.83	37	LMR, ACO
5	265	0.67	0.83	27	LMR, ACO

Interfaces

17 interfaces between chains.

C–E · 3662 Å² buried · 45 hydrogen bonds · protein-protein
A–G · 3659 Å² buried · 44 hydrogen bonds · protein-protein
B–H · 3645 Å² buried · 45 hydrogen bonds · protein-protein
D–F · 3641 Å² buried · 45 hydrogen bonds · protein-protein
F–H · 2377 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

6QCL · Citryl-CoA lyase core module of Chlorobium limicola ATP citrate lyase in complex with… · 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 Q9AJC4
Elsewhere: RCSB PDB 6QCL · PDBe 6QCL · UniProt Q9AJC4

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