MolNFT v1 · #174734 · protein
Sphingosine-1-phosphate receptor 3 with a natural ligand.
7C4S · Antibody Fab fragment light chain: “Sphingosine-1-phosphate receptor 3 with a natural ligand.”. X-ray diffraction, 1 ligand (S1P), 17 pockets (best druggability 0.82). MolNFT v1 #174734 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7C4S
- Type
- protein
- Length
- 1,428 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment light chain; Antibody Fab fragment heavy chain; Sphingosine…
- UniProt
- Q99500
- Ligands
- S1P
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, K | Antibody Fab fragment light chain | protein | 214 | 6% helix, 51% strand | — |
| H, J | Antibody Fab fragment heavy chain | protein | 219 | 5% helix, 52% strand | — |
| A | Sphingosine 1-phosphate receptor 3 | protein | 282 | 68% helix, 1% strand | Q99500 |
| B | Sphingosine 1-phosphate receptor 3 | protein | 280 | 68% helix, 1% strand | Q99500 |
Ligands and binding sites
- S1P · (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · 2 copies · chains A, B
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 | 790 | 0.82 | 0.85 | 74 | S1P |
| 2 | 750 | 0.81 | 0.84 | 69 | S1P |
| 3 | 947 | 0.71 | 0.76 | 113 | empty |
| 4 | 549 | 0.67 | 0.78 | 66 | empty |
| 5 | 294 | 0.57 | 0.76 | 39 | empty |
Interfaces
10 interfaces between chains.
- K–J · 2020 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 2017 Ų buried · 19 hydrogen bonds · protein-protein
- J–B · 631 Ų buried · 7 hydrogen bonds · protein-protein
- H–J · 630 Ų buried · 8 hydrogen bonds · protein-protein
- H–A · 626 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7C4S · Sphingosine-1-phosphate receptor 3 with a natural ligand. · the same entry in another collection · chain B against B, TM-score 1.00
- Q99500 · AlphaFold monomer V2.0 prediction for sphingosine 1-phosphate receptor 3 (Q99500) · 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 Q99500
- Elsewhere: RCSB PDB 7C4S · PDBe 7C4S · UniProt Q99500
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