MolNFT v1 · #152392 · protein
Structure of mitochondrial cdp-dag synthase TAM41, delta 74
6IG4 · Phosphatidate cytidylyltransferase, mitochondrial: “Structure of mitochondrial cdp-dag synthase TAM41, delta 74”. X-ray diffraction, 2 ligands (3G0, PT), 6 pockets (best druggability 0.81). MolNFT v1 #152392 on GenesisL1: 3D…
- PDB
- 6IG4
- Type
- protein
- Length
- 549 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidate cytidylyltransferase, mitochondrial
- EC
- 2.7.7.41
- UniProt
- O74339
- Ligands
- 3G0, PT
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidate cytidylyltransferase, mitochondrial (EC 2.7.7.41) | protein | 277 | 49% helix, 16% strand | O74339 |
| B | Phosphatidate cytidylyltransferase, mitochondrial (EC 2.7.7.41) | protein | 272 | 48% helix, 16% strand | O74339 |
Ligands and binding sites
- 3G0 · tetracyanoplatinate(II) · ligand · 3 copies · chains A, B
- PT · Platinum (II) ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.81 | 0.97 | 26 | empty |
| 2 | 177 | 0.72 | 0.89 | 25 | 3G0 |
| 3 | 167 | 0.69 | 0.88 | 30 | 3G0 |
| 4 | 155 | 0.64 | 0.86 | 23 | empty |
| 5 | 110 | 0.37 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1374 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6IG4 · Structure of mitochondrial CDP-DAG synthase Tam41, delta 74 · 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 B 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 6IG4 · PDBe 6IG4 · UniProt O74339
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