MolNFT v1 · #15326 · protein
Glycerol-3-phosphate cytidylyltransferase complexed with cdp-glycerol
1N1D: “Glycerol-3-phosphate cytidylyltransferase complexed with cdp-glycerol”. X-ray diffraction, 2 ligands (C2G, SO4), 5 pockets (best druggability 0.73). MolNFT v1 #15326 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1N1D
- Type
- protein
- Length
- 504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol-3-phosphate cytidylyltransferase
- EC
- 2.7.7.39
- UniProt
- P27623
- Ligands
- C2G, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycerol-3-phosphate cytidylyltransferase (EC 2.7.7.39) | protein | 126 | 37% helix, 23% strand | P27623 |
Ligands and binding sites
- C2G · [cytidine-5'-phosphate] glycerylphosphoric acid ester · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.73 | 0.85 | 42 | SO4, C2G |
| 2 | 306 | 0.72 | 0.85 | 37 | SO4, C2G |
| 3 | 373 | 0.72 | 0.83 | 45 | C2G |
| 4 | 283 | 0.69 | 0.84 | 37 | SO4, C2G |
| 5 | 58 | 0.31 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1126 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1081 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1N1D · Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol · the same entry in another collection · chain A against A, TM-score 1.00
- P27623 · AlphaFold monomer V2.0 prediction for glycerol-3-phosphate cytidylyltransferase (P27623) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P27623
- Elsewhere: RCSB PDB 1N1D · PDBe 1N1D · UniProt P27623
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