Research workbench

Crystal structure of chicken md-1

Analyse Crystal structure of chicken md-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MTX
Type: protein
Length: 278 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein md-1
UniProt: Q90890
Ligands: PGT
Pockets: 2 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein md-1	protein	138	4% helix, 56% strand	Q90890
B	Protein md-1	protein	140	4% helix, 55% strand	Q90890

Ligands and binding sites

PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 2 copies · chains A, B
PGE · Triethylene glycol · additive · chains A, B
GOL · Glycerol · additive · chains 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	609	0.82	0.86	58	PGT
2	568	0.81	0.86	54	PGT

Interfaces

1 interface between chains.

A–B · 403 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3MTX · Crystal structure of chicken MD-1 · the same entry in another collection · chain A against A, TM-score 1.00
Q90890 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 86 (Q90890) · 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 Q90890
Elsewhere: RCSB PDB 3MTX · PDBe 3MTX · UniProt Q90890

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