Research workbench
Cryo-EM structure of human ATP-citrate lyase in complex with inhibitor ndi-091143
Analyse Cryo-EM structure of human ATP-citrate lyase in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O0H
- Type
- protein
- Length
- 4,092 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
- LBG, ADP
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ATP-citrate synthase (EC 2.3.3.8) | protein | 1023 | 38% helix, 16% strand | P53396 |
Ligands and binding sites
- LBG · Methyl 3-chloro-5-[(4,6-difluoro[1,1'-biphenyl]-3-yl) sulfamoyl]-4-hydroxybenzoate · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
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 | 257 | 0.83 | 0.95 | 37 | LBG |
| 2 | 253 | 0.83 | 0.94 | 36 | LBG |
| 3 | 559 | 0.81 | 0.87 | 70 | LBG |
| 4 | 1087 | 0.80 | 0.82 | 127 | LBG |
| 5 | 583 | 0.76 | 0.83 | 67 | empty |
Interfaces
6 interfaces between chains.
- B–D · 4499 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 4495 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2354 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2353 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1895 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6O0H · Cryo-EM structure of human ATP-citrate lyase in complex with inhibitor NDI-091143 · the same entry in another collection · chain A against A, 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 0.86
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 6O0H · PDBe 6O0H · UniProt P53396
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