Research workbench
Structure of the citryl-CoA lyase core module of chlorobium limicola ATP citrate lyase (space group P21)
Analyse Structure of the citryl-CoA lyase core module of chlorobium limicola ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HXO
- Type
- protein
- Length
- 1,986 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-citrate lyase alpha-subunit
- UniProt
- Q9AJC4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | ATP-citrate lyase alpha-subunit | protein | 260 | 55% helix, 7% strand | Q9AJC4 |
| B | ATP-citrate lyase alpha-subunit | protein | 261 | 54% helix, 7% strand | Q9AJC4 |
| C, G, H | ATP-citrate lyase alpha-subunit | protein | 256 | 56% helix, 6% strand | Q9AJC4 |
| D | ATP-citrate lyase alpha-subunit | protein | 257 | 56% helix, 6% strand | Q9AJC4 |
| E | ATP-citrate lyase alpha-subunit | protein | 180 | 53% helix, 8% strand | Q9AJC4 |
Ligands and binding sites
- FLC · Citrate anion · additive · 6 copies · chains A, E, B, F, C, G, D, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.74 | 0.77 | 93 | empty |
| 2 | 414 | 0.68 | 0.80 | 41 | FLC |
| 3 | 350 | 0.66 | 0.80 | 40 | FLC |
| 4 | 344 | 0.66 | 0.80 | 37 | FLC |
| 5 | 301 | 0.65 | 0.81 | 39 | FLC |
Interfaces
17 interfaces between chains.
- A–G · 3730 Ų buried · 48 hydrogen bonds · protein-protein
- B–H · 3721 Ų buried · 49 hydrogen bonds · protein-protein
- D–F · 3687 Ų buried · 48 hydrogen bonds · protein-protein
- C–E · 3485 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 2424 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6HXO · Structure of the citryl-CoA lyase core module of Chlorobium limicola ATP citrate lyase… · the same entry in another collection · chain D against D, 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 Q9AJC4
- Elsewhere: RCSB PDB 6HXO · PDBe 6HXO · UniProt Q9AJC4
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