MolNFT v1 · #152391 · protein
Structure of mitochondrial cdp-dag synthase TAM41 complexed with CTP, delta 74, F240A
6IG2 · Phosphatidate cytidylyltransferase, mitochondrial: “Structure of mitochondrial cdp-dag synthase TAM41 complexed with CTP, delta 74, F240A”. X-ray diffraction, 1 ligand (CTP), 17 pockets (best druggability 0.80). MolNFT v1 #152391 on…
- PDB
- 6IG2
- Type
- protein
- Length
- 1,100 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidate cytidylyltransferase, mitochondrial
- EC
- 2.7.7.41
- UniProt
- O74339
- Ligands
- CTP
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphatidate cytidylyltransferase, mitochondrial (EC 2.7.7.41) | protein | 272 | 44% helix, 16% strand | O74339 |
| C, D | Phosphatidate cytidylyltransferase, mitochondrial (EC 2.7.7.41) | protein | 278 | 47% helix, 15% strand | O74339 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.80 | 0.97 | 25 | empty |
| 2 | 406 | 0.78 | 0.87 | 42 | empty |
| 3 | 486 | 0.78 | 0.85 | 43 | CTP |
| 4 | 123 | 0.78 | 0.96 | 23 | empty |
| 5 | 111 | 0.66 | 0.90 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1448 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1323 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 441 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 408 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6IG2 · Structure of mitochondrial CDP-DAG synthase Tam41 complexed with CTP, delta 74, F240A · the same entry in another collection · chain A against A, TM-score 1.00
- O74339 · AlphaFold monomer V2.0 prediction for phosphatidate cytidylyltransferase, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 O74339
- Elsewhere: RCSB PDB 6IG2 · PDBe 6IG2 · UniProt O74339
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