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Structure of the human ATP citrate lyase holoenzyme in complex with citrate, coenzyme A and Mg.ADP
Analyse Structure of the human ATP citrate lyase holoenzyme in complex with citrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HXH
- Type
- protein
- Length
- 8,264 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Homo sapiens
- Molecule
- ATP-citrate synthase,Human ATP citrate lyase
- EC
- 2.3.3.8
- UniProt
- P53396
- Ligands
- COA, ADP, MG, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 3.3 · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | ATP-citrate synthase,Human ATP citrate lyase (EC 2.3.3.8) | protein | 1033 | 42% helix, 18% strand | P53396 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- FLC · Citrate anion · additive · 8 copies · chains A, B, C, D, E, F, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.85 | 0.87 | 129 | MG, PO4, FLC, ADP |
| 2 | 1079 | 0.84 | 0.85 | 123 | ADP, MG |
| 3 | 827 | 0.83 | 0.86 | 94 | ADP, MG |
| 4 | 568 | 0.83 | 0.89 | 77 | MG, PO4, FLC |
| 5 | 792 | 0.83 | 0.86 | 98 | ADP, MG |
Interfaces
16 interfaces between chains.
- A–B · 4641 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 4582 Ų buried · 47 hydrogen bonds · protein-protein
- G–H · 4582 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 4578 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 2424 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 6HXH · Structure of the human ATP citrate lyase holoenzyme in complex with citrate, coenzyme a… · the same entry in another collection · chain H against H, TM-score 1.00
- P53396 · AlphaFold monomer V2.0 prediction for ATP-citrate synthase (P53396) · 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 P53396
- Elsewhere: RCSB PDB 6HXH · PDBe 6HXH · UniProt P53396
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