MolNFT v1 · #71224 · protein

Crystal structure of mouse md-1 in complex with phosphatidylcholine

3M7O · Lymphocyte antigen 86: “Crystal structure of mouse md-1 in complex with phosphatidylcholine”. X-ray diffraction, 3 ligands (BEN, L9R, NAG), 3 pockets (best druggability 0.88). MolNFT v1 #71224 on GenesisL1: 3D structure, binding…

PDB: 3M7O
Type: protein
Length: 530 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lymphocyte antigen 86
UniProt: O88188
Ligands: BEN, L9R, NAG
Pockets: 3 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lymphocyte antigen 86	protein	137	0% helix, 59% strand	O88188
B, C, D	Lymphocyte antigen 86	protein	131	0% helix, 56% strand	O88188

Ligands and binding sites

BEN · Benzamidine · ligand · 16 copies · chains A, D, B, C
L9R · (2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 2 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, D, C

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1062	0.88	0.88	87	L9R
2	1043	0.88	0.88	90	L9R
3	1178	0.78	0.80	121	NAG, BEN

Interfaces

5 interfaces between chains.

C–D · 525 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 490 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 252 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 188 Å² buried · 1 hydrogen bond · protein-protein
A–C · 179 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

3M7O · Crystal structure of mouse MD-1 in complex with phosphatidylcholine · the same entry in another collection · chain A against A, TM-score 1.00
O88188 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 86 (O88188) · a predicted model of the same protein · chain B 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 O88188
Elsewhere: RCSB PDB 3M7O · PDBe 3M7O · UniProt O88188

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.