MolNFT v1 · #55299 · protein

Structure of apolioprotein M in complex with sphingosine 1-phosphate

2YG2 · Apolipoprotein M: “Structure of apolioprotein M in complex with sphingosine 1-phosphate”. X-ray diffraction, 1 ligand (S1P), 2 pockets (best druggability 0.80). MolNFT v1 #55299 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2YG2
Type: protein
Length: 313 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apolipoprotein M
UniProt: O95445
Ligands: S1P
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apolipoprotein M	protein	162	15% helix, 45% strand	O95445
B	Apolipoprotein M	protein	151	17% helix, 48% strand	O95445

Ligands and binding sites

S1P · (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · 2 copies · chains A, B
FLC · Citrate anion · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	684	0.80	0.84	79	S1P, FLC
2	259	0.79	0.90	31	S1P

Interfaces

1 interface between chains.

A–B · 344 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

2YG2 · Structure of apolioprotein M in complex with Sphingosine 1-Phosphate · the same entry in another collection · chain A against A, TM-score 1.00
O95445 · AlphaFold monomer V2.0 prediction for apolipoprotein M (O95445) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 O95445
Elsewhere: RCSB PDB 2YG2 · PDBe 2YG2 · UniProt O95445

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