Research workbench
Structural determination of the A50T:S279G:S280K:V281K:K282E:H283N variant of citrate synthase from E. COLI complexed with oxaloacetate
Analyse Structural determination of the A50T:S279G:S280K:V281K:K282E:H283N variant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JAG
- Type
- protein
- Length
- 852 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Citrate synthase
- EC
- 2.3.3.1
- UniProt
- P0ABH7
- Ligands
- OAA, SO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Citrate synthase (EC 2.3.3.1) | protein | 426 | 51% helix, 9% strand | P0ABH7 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.82 | 0.83 | 98 | OAA |
| 2 | 978 | 0.80 | 0.82 | 111 | OAA |
| 3 | 146 | 0.78 | 0.95 | 33 | empty |
| 4 | 60 | 0.56 | 0.89 | 20 | empty |
| 5 | 132 | 0.52 | 0.81 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 6248 Ų buried · 109 hydrogen bonds · protein-protein
Compared structures
- 4JAG · STRUCTURAL DETERMINATION OF THE A50T:S279G:S280K:V281K:K282E:H283N VARIANT OF CITRATE… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABH7 · AlphaFold monomer V2.0 prediction for citrate synthase (P0ABH7) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P0ABH7
- Elsewhere: RCSB PDB 4JAG · PDBe 4JAG · UniProt P0ABH7
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