Research workbench
Citryl-CoA lyase module of human ATP citrate lyase in complex with (3S)-citryl-CoA.
Analyse Citryl-CoA lyase module of human ATP citrate lyase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z2H
- Type
- protein
- Length
- 1,049 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
- Q5B, OAA, ACO
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-citrate synthase (EC 2.3.3.8) | protein | 264 | 59% helix, 7% strand | P53396 |
| B | ATP-citrate synthase (EC 2.3.3.8) | protein | 261 | 59% helix, 6% strand | P53396 |
| C | ATP-citrate synthase (EC 2.3.3.8) | protein | 263 | 58% helix, 7% strand | P53396 |
| D | ATP-citrate synthase (EC 2.3.3.8) | protein | 261 | 59% helix, 7% strand | P53396 |
Ligands and binding sites
- Q5B · (3S)-citryl-Coenzyme A · ligand · 3 copies · chains A, D, B, C
- OAA · Oxaloacetate ion · ligand · 2 copies · chains A, D, B, C
- ACO · Acetyl coenzyme *A · ligand · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.69 | 0.83 | 34 | Q5B, OAA, ACO |
| 2 | 260 | 0.68 | 0.84 | 32 | Q5B, OAA, ACO |
| 3 | 350 | 0.65 | 0.79 | 40 | empty |
| 4 | 362 | 0.64 | 0.79 | 36 | Q5B |
| 5 | 245 | 0.51 | 0.76 | 37 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3459 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 3453 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1632 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1533 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1352 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- P53396 · AlphaFold monomer V2.0 prediction for ATP-citrate synthase (P53396) · a predicted model of the same protein · chain B 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 P53396
- Elsewhere: RCSB PDB 6Z2H · PDBe 6Z2H · UniProt P53396
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