MolNFT v1 · #173494 · protein
Crystal structure of phosphatidyl serine synthase (pss) in the closed conformation with bound citrate.
7B1N · Cdp-diacylglycerol--serine O-phosphatidyltransferase: “Crystal structure of phosphatidyl serine synthase (pss) in the closed conformation with bound citrate.”. X-ray diffraction, 3 ligands (58A, CA, CL), 3 pockets (best druggability…
- PDB
- 7B1N
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdp-diacylglycerol--serine O-phosphatidyltransferase
- EC
- 2.7.8.8
- UniProt
- Q58609
- Ligands
- 58A, CA, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cdp-diacylglycerol--serine O-phosphatidyltransferase (EC 2.7.8.8) | protein | 200 | 76% helix, 2% strand | Q58609 |
Ligands and binding sites
- 58A · 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9e)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy) phosphoryl]cytidine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.76 | 0.82 | 55 | 58A, CL |
| 2 | 615 | 0.75 | 0.82 | 50 | 58A, CL |
| 3 | 53 | 0.29 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1969 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7B1N · Crystal structure of phosphatidyl serine synthase (PSS) in the closed conformation with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58609 · AlphaFold monomer V2.0 prediction for cdp-diacylglycerol--serine… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q58609
- Elsewhere: RCSB PDB 7B1N · PDBe 7B1N · UniProt Q58609
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