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Structure of a chondroitin sulphate binding DBL3X from a VAR2CSA encoded PFEMP1 protein in complex with sulphate

Analyse Structure of a chondroitin sulphate binding DBL3X from a VAR2CSA encoded PFEMP1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BQK
Type: protein
Length: 338 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Erythrocyte membrane protein 1
UniProt: Q6UDW7
Ligands: SO4
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Erythrocyte membrane protein 1	protein	338	54% helix, 8% strand	Q6UDW7

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · additive · chains A

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

Pockets

5 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	142	0.64	0.86	30	empty
2	262	0.51	0.74	33	empty
3	136	0.50	0.79	19	empty
4	116	0.42	0.77	23	GOL
5	69	0.31	0.75	21	empty

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3BQK · Structure of a chondroitin sulphate binding DBL3X from a var2csa encoded PfEMP1 protein… · the same entry in another collection · 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 Q6UDW7
Elsewhere: RCSB PDB 3BQK · PDBe 3BQK · UniProt Q6UDW7

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