Research workbench
Structure of ATP citrate lyase from chlorobium limicola in complex with citrate and coenzyme a.
Analyse Structure of ATP citrate lyase from chlorobium limicola 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
- 6HXJ
- Type
- protein
- Length
- 3,661 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-citrate lyase beta-subunit; ATP-citrate lyase alpha-subunit
- UniProt
- Q9AQH6, Q9AJC4
- Ligands
- COA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-citrate lyase beta-subunit | protein | 336 | 37% helix, 27% strand | Q9AQH6 |
| B | ATP-citrate lyase alpha-subunit | protein | 589 | 46% helix, 15% strand | Q9AJC4 |
| C | ATP-citrate lyase beta-subunit | protein | 324 | 40% helix, 25% strand | Q9AQH6 |
| D, H | ATP-citrate lyase alpha-subunit | protein | 591 | 46% helix, 15% strand | Q9AJC4 |
| E | ATP-citrate lyase beta-subunit | protein | 320 | 38% helix, 24% strand | Q9AQH6 |
| F | ATP-citrate lyase alpha-subunit | protein | 588 | 46% helix, 15% strand | Q9AJC4 |
| G | ATP-citrate lyase beta-subunit | protein | 322 | 39% helix, 25% strand | Q9AQH6 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 8 copies · chains B, A, H, D, E, F, G
- FLC · Citrate anion · additive · 8 copies · chains A, B, F, C, D, H, E, G
- PGE · Triethylene glycol · additive · 5 copies · chains B, C, D, F, H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, D, F, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains C, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.77 | 0.79 | 106 | FLC |
| 2 | 1182 | 0.75 | 0.78 | 117 | FLC, TRS |
| 3 | 746 | 0.75 | 0.80 | 78 | FLC |
| 4 | 488 | 0.70 | 0.80 | 57 | FLC |
| 5 | 53 | 0.68 | 0.97 | 20 | empty |
Interfaces
13 interfaces between chains.
- D–F · 3950 Ų buried · 54 hydrogen bonds · protein-protein
- B–H · 3918 Ų buried · 49 hydrogen bonds · protein-protein
- D–H · 2765 Ų buried · 22 hydrogen bonds · protein-protein
- F–H · 2718 Ų buried · 37 hydrogen bonds · protein-protein
- B–F · 2676 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6HXJ · Structure of ATP citrate lyase from Chlorobium limicola in complex with citrate and… · the same entry in another collection · chain A 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 Q9AQH6
- Every structure of UniProt Q9AJC4
- Elsewhere: RCSB PDB 6HXJ · PDBe 6HXJ · UniProt Q9AQH6 · UniProt Q9AJC4
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