MolNFT v1 · #96115 · protein
Structural determination of the A50T:S279G:S280K:V281K:K282E:H283N variant of citrate synthase from E. COLI complexed with NADH
4JAF: “Structural determination of the A50T:S279G:S280K:V281K:K282E:H283N variant of citrate synthase from E. COLI…”. X-ray diffraction, 2 ligands (NAI, SO4), 13 pockets (best druggability 0.82). MolNFT v1 #96115 on GenesisL1: 3D…
- PDB
- 4JAF
- 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
- NAI, SO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Citrate synthase (EC 2.3.3.1) | protein | 426 | 50% helix, 10% strand | P0ABH7 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · 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
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.82 | 0.94 | 40 | empty |
| 2 | 873 | 0.81 | 0.84 | 90 | SO4 |
| 3 | 696 | 0.78 | 0.83 | 87 | SO4 |
| 4 | 53 | 0.63 | 0.93 | 16 | empty |
| 5 | 77 | 0.58 | 0.88 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 6335 Ų buried · 102 hydrogen bonds · protein-protein
Compared structures
- 4JAF · 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 4JAF · PDBe 4JAF · UniProt P0ABH7
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