Research workbench
Crystal structure of an intramembrane cdp-dag synthetase central for phospholipid biosynthesis (S200C/S223C, inactive mutant)
Analyse Crystal structure of an intramembrane cdp-dag synthetase central for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q2G
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidate cytidylyltransferase
- EC
- 2.7.7.41
- UniProt
- Q9X1B7
- Ligands
- BNG, HG, MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidate cytidylyltransferase (EC 2.7.7.41) | protein | 261 | 75% helix, 1% strand | Q9X1B7 |
| B | Phosphatidate cytidylyltransferase (EC 2.7.7.41) | protein | 269 | 76% helix, 1% strand | Q9X1B7 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- HG · Mercury (II) ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.67 | 0.79 | 59 | MG, BNG |
| 2 | 492 | 0.67 | 0.78 | 56 | MG, BNG |
| 3 | 196 | 0.47 | 0.75 | 32 | empty |
| 4 | 50 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2043 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Q2G · CRYSTAL STRUCTURE OF AN INTRAMEMBRANE CDP-DAG SYNTHETASE CENTRAL FOR PHOSPHOLIPID… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1B7 · AlphaFold monomer V2.0 prediction for phosphatidate cytidylyltransferase (Q9X1B7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9X1B7
- Elsewhere: RCSB PDB 4Q2G · PDBe 4Q2G · UniProt Q9X1B7
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