MolNFT v1 · #125685 · protein

The cidra domain from MCVAR1 PFEMP1 bound to CD36

5LGD · Platelet glycoprotein 4: “The cidra domain from MCVAR1 PFEMP1 bound to CD36”. X-ray diffraction, 3 ligands (PLM, NAG, MAN), 5 pockets (best druggability 0.87). MolNFT v1 #125685 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5LGD
Type: protein
Length: 551 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Platelet glycoprotein 4; PFEMP1 variant 1 of strain mc
UniProt: P16671, Q25733
Ligands: PLM, NAG, MAN
Pockets: 5 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Platelet glycoprotein 4	protein	400	24% helix, 34% strand	P16671
B	PFEMP1 variant 1 of strain mc	protein	151	68% helix, 0% strand	Q25733

Ligands and binding sites

PLM · Palmitic acid · ligand · 2 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
MAN · alpha-D-mannopyranose · sugar
GOL · Glycerol · additive · 5 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1127	0.87	0.88	134	PLM
2	102	0.43	0.78	14	NAG
3	59	0.40	0.81	16	empty
4	50	0.39	0.81	12	TRS
5	81	0.36	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 708 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

5LGD · The CIDRa domain from MCvar1 PfEMP1 bound to CD36 · the same entry in another collection · chain A against A, TM-score 1.00
P16671 · AlphaFold monomer V2.0 prediction for platelet glycoprotein 4 (P16671) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P16671
Every structure of UniProt Q25733
Elsewhere: RCSB PDB 5LGD · PDBe 5LGD · UniProt P16671 · UniProt Q25733

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