MolNFT v1 · #151766 · protein
Structure of ATP citrate lyase from methanothrix soehngenii in complex with citrate and coenzyme a
6HXI · Citrate lyase, subunit 1: “Structure of ATP citrate lyase from methanothrix soehngenii in complex with citrate and coenzyme a”. X-ray diffraction, 2 ligands (COA, NA), 20 pockets (best druggability 0.80). MolNFT v1 #151766 on…
- PDB
- 6HXI
- Type
- protein
- Length
- 2,023 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate lyase, subunit 1; Succinyl-CoA ligase (ADP-forming) subunit alpha
- EC
- 2.3.3.8, 6.2.1.5
- UniProt
- A0A0W8FB26, A0A1V4VDZ9
- Ligands
- COA, NA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Citrate lyase, subunit 1 (EC 2.3.3.8) | protein | 381 | 34% helix, 26% strand | A0A0W8FB26 |
| B, D | Succinyl-CoA ligase (ADP-forming) subunit alpha (EC 6.2.1.5) | protein | 616 | 45% helix, 13% strand | A0A1V4VDZ9 |
| C | Citrate lyase, subunit 1 (EC 2.3.3.8) | protein | 410 | 35% helix, 26% strand | A0A0W8FB26 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains B, C, A, D
- NA · Sodium ion · metal · 2 copies · chains A, C
- ACT · Acetate ion · additive · 3 copies · chains B, D
- FLC · Citrate anion · additive · 2 copies · chains A, D, B, C
- PGE · Triethylene glycol · additive · 2 copies · chains B, D
- PG4 · Tetraethylene glycol · additive · chains B
- SIN · Succinic acid · additive · chains 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.80 | 0.83 | 82 | NA |
| 2 | 962 | 0.78 | 0.80 | 88 | NA |
| 3 | 312 | 0.73 | 0.86 | 43 | FLC |
| 4 | 338 | 0.71 | 0.84 | 47 | FLC |
| 5 | 331 | 0.66 | 0.81 | 38 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2581 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 2552 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2452 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 6HXI · Structure of ATP citrate lyase from Methanothrix soehngenii in complex with citrate and… · the same entry in another collection · chain B against B, 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 A0A0W8FB26
- Every structure of UniProt A0A1V4VDZ9
- Elsewhere: RCSB PDB 6HXI · PDBe 6HXI · UniProt A0A0W8FB26 · UniProt A0A1V4VDZ9
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