Research workbench
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
- 6QFB
- Type
- protein
- Length
- 4,090 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-citrate synthase
- EC
- 2.3.3.8
- UniProt
- P53396
- Ligands
- COA, ADP, MG, 2HP
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-citrate synthase (EC 2.3.3.8) | protein | 1019 | 42% helix, 17% strand | P53396 |
| B | ATP-citrate synthase (EC 2.3.3.8) | protein | 1035 | 43% helix, 17% strand | P53396 |
| C | ATP-citrate synthase (EC 2.3.3.8) | protein | 1011 | 41% helix, 17% strand | P53396 |
| D | ATP-citrate synthase (EC 2.3.3.8) | protein | 1025 | 42% helix, 18% strand | P53396 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- 2HP · Dihydrogenphosphate ion · ion · 3 copies · chains A, B, D
- FLC · Citrate anion · additive · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.78 | 0.83 | 73 | COA, 2HP, FLC, MG |
| 2 | 424 | 0.76 | 0.85 | 62 | ADP, MG |
| 3 | 58 | 0.74 | 0.99 | 16 | empty |
| 4 | 965 | 0.72 | 0.76 | 95 | empty |
| 5 | 884 | 0.70 | 0.76 | 95 | 2HP |
Interfaces
2 interfaces between chains.
- A–B · 4417 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2383 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 6QFB · Structure of the human ATP citrate lyase holoenzyme in complex with citrate, coenzyme A… · 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 B against A, TM-score 0.97
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 6QFB · PDBe 6QFB · UniProt P53396
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