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Local refinement of human ATP citrate lyase E599Q mutant ash domain

Analyse Local refinement of human ATP citrate lyase E599Q mutant ash domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LIW
Type: protein
Length: 1,871 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-citrate synthase
EC: 2.3.3.8
UniProt: P53396
Ligands: ADP, COA, Y2A
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 2 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	ATP-citrate synthase (EC 2.3.3.8)	protein	279	55% helix, 7% strand	P53396
B	ATP-citrate synthase (EC 2.3.3.8)	protein	1034	39% helix, 18% strand	P53396

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains B
COA · Coenzyme A · ligand · chains B, D
Y2A · (2S)-2-hydroxy-2-[2-oxo-2-(phosphonooxy) ethyl]butanedioic acid · ligand · chains B

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1086	0.83	0.84	135	ADP
2	959	0.83	0.84	109	COA, Y2A
3	492	0.67	0.78	51	empty
4	481	0.66	0.78	50	empty
5	327	0.66	0.81	41	empty

Interfaces

6 interfaces between chains.

B–D · 4022 Å² buried · 39 hydrogen bonds · protein-protein
A–C · 3411 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 2198 Å² buried · 39 hydrogen bonds · protein-protein
A–D · 1996 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1835 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

7LIW · Local refinement of human ATP citrate lyase E599Q mutant ASH domain · the same entry in another collection · chain D against D, TM-score 1.00
P53396 · AlphaFold monomer V2.0 prediction for ATP-citrate synthase (P53396) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P53396
Elsewhere: RCSB PDB 7LIW · PDBe 7LIW · UniProt P53396

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