Research workbench
Structure of wild type human PSS1
Analyse Structure of wild type human PSS1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9B4E
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Phosphatidylserine synthase 1
- EC
- 2.7.8.29
- UniProt
- P48651
- Ligands
- P5S, LBN, A1AIS, 6OU, CA
- Pockets
- 11 · best druggability 0.84
Structure
electron microscopy · resolution 2.7 · 1 distinct chain · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphatidylserine synthase 1 (EC 2.7.8.29) | protein | 389 | 71% helix, 1% strand | P48651 |
Ligands and binding sites
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · 4 copies · chains A, B
- LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, B
- A1AIS · (2R)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate · ligand · 2 copies · chains A, B
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.84 | 0.86 | 74 | 6OU, CA |
| 2 | 692 | 0.83 | 0.87 | 77 | 6OU, CA |
| 3 | 536 | 0.72 | 0.80 | 44 | A1AIS |
| 4 | 528 | 0.71 | 0.80 | 45 | A1AIS |
| 5 | 306 | 0.70 | 0.82 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2700 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- P48651 · AlphaFold monomer V2.0 prediction for phosphatidylserine synthase 1 (P48651) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P48651
- Elsewhere: RCSB PDB 9B4E · PDBe 9B4E · UniProt P48651
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