MolNFT v1 · #151769 · protein
Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate and coash (space group P21)
6HXL · ATP-citrate synthase: “Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate and coash…”. X-ray diffraction, 3 ligands (COA, CAO, SO4), 20 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 6HXL
- Type
- protein
- Length
- 2,098 residues
- Chains
- 8
- 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, CAO, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | ATP-citrate synthase (EC 2.3.3.8) | protein | 263 | 59% helix, 7% strand | P53396 |
| B, E | 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 | 262 | 58% helix, 7% strand | P53396 |
| G | ATP-citrate synthase (EC 2.3.3.8) | protein | 262 | 59% helix, 7% strand | P53396 |
| H | ATP-citrate synthase (EC 2.3.3.8) | protein | 264 | 58% helix, 6% strand | P53396 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 7 copies · chains A, B, C, D, E, G, H
- CAO · Oxidized coenzyme A · ligand · chains F
- SO4 · Sulfate ion · ion · 2 copies · chains D, E, H
- FLC · Citrate anion · additive · 5 copies · chains A, B, C, D, E, G
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C, E, F
- EDO · 1,2-ethanediol · additive · chains 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.77 | 0.79 | 90 | SO4 |
| 2 | 51 | 0.73 | 1.00 | 17 | empty |
| 3 | 50 | 0.73 | 0.99 | 18 | empty |
| 4 | 333 | 0.68 | 0.82 | 38 | COA, FLC |
| 5 | 315 | 0.67 | 0.82 | 36 | COA, FLC |
Interfaces
17 interfaces between chains.
- A–D · 3511 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 3511 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 3488 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 3434 Ų buried · 26 hydrogen bonds · protein-protein
- E–G · 1668 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6HXL · Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with… · 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 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 6HXL · PDBe 6HXL · UniProt P53396
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