Research workbench
Structure of human ATP citrate lyase E599Q mutant in complex with MG2+, citrate, ATP and CoA
Analyse Structure of human ATP citrate lyase E599Q mutant in complex with MG2+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UUW
- Type
- protein
- Length
- 4,136 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
- ADP, COA, Y2A, UNL
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ATP-citrate synthase (EC 2.3.3.8) | protein | 1034 | 39% helix, 18% strand | P53396 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- COA · Coenzyme A · ligand · 4 copies · chains A, C, B, D
- Y2A · (2S)-2-hydroxy-2-[2-oxo-2-(phosphonooxy) ethyl]butanedioic acid · ligand · 4 copies · chains A, B, C, D
- UNL · Unknown ligand · ion · 2 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 | 1043 | 0.83 | 0.84 | 126 | ADP |
| 2 | 1065 | 0.83 | 0.84 | 126 | ADP |
| 3 | 1143 | 0.81 | 0.82 | 119 | COA, Y2A |
| 4 | 1118 | 0.81 | 0.82 | 117 | COA, Y2A |
| 5 | 1074 | 0.81 | 0.82 | 111 | ADP |
Interfaces
6 interfaces between chains.
- A–C · 4783 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 4782 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2518 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2509 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 1938 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6UUW · Structure of human ATP citrate lyase E599Q mutant in complex with Mg2+, citrate, ATP and… · 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 6UUW · PDBe 6UUW · UniProt P53396
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