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Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate
Analyse Structure of the citryl-CoA lyase core module of human ATP citrate lyase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HXK
- Type
- protein
- Length
- 1,043 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens
- Molecule
- ATP-citrate synthase
- EC
- 2.3.3.8
- UniProt
- P53396
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.85 · 3 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-citrate synthase (EC 2.3.3.8) | protein | 262 | 59% helix, 6% strand | P53396 |
| B | ATP-citrate synthase (EC 2.3.3.8) | protein | 261 | 59% helix, 7% strand | P53396 |
| C, D | ATP-citrate synthase (EC 2.3.3.8) | protein | 260 | 59% helix, 6% strand | P53396 |
Ligands and binding sites
- FLC · Citrate anion · additive · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.69 | 0.80 | 41 | FLC |
| 2 | 435 | 0.68 | 0.80 | 41 | FLC |
| 3 | 491 | 0.68 | 0.79 | 43 | FLC |
| 4 | 362 | 0.66 | 0.80 | 41 | FLC |
| 5 | 312 | 0.56 | 0.76 | 37 | PGE |
Interfaces
6 interfaces between chains.
- A–B · 3534 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 3470 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1435 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1413 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1404 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6HXK · Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with… · 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 6HXK · PDBe 6HXK · UniProt P53396
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