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Crystal structure of VAR2CSA DBL3X domain in the presence of dodecasaccharide of csa

Analyse Crystal structure of VAR2CSA DBL3X domain in the presence of dodecasaccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CPZ
Type: protein
Length: 297 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: 4 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Erythrocyte membrane protein 1	protein	297	52% helix, 1% strand	Q6UDW7

Ligands and binding sites

SO4 · Sulfate ion · ion

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

Pockets

4 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	219	0.64	0.83	33	empty
2	112	0.49	0.80	19	empty
3	68	0.43	0.81	19	empty
4	147	0.42	0.74	24	empty

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3CPZ · Crystal structure of VAR2CSA DBL3x domain in the presence of dodecasaccharide of CSA · 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 3CPZ · PDBe 3CPZ · UniProt Q6UDW7

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