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Structure of DBL6 epsilon domain from VAR2CSA strain FCR3

Analyse Structure of DBL6 epsilon domain from VAR2CSA strain FCR3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Y8D
Type: protein
Length: 281 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Erythrocyte membrane protein 1
UniProt: Q6UDW7
Ligands: DHL, BEN
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 63% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Erythrocyte membrane protein 1	protein	281	63% helix, 4% strand	Q6UDW7

Ligands and binding sites

DHL · 2-amino-ethanethiol · ligand · 2 copies · chains A
BEN · Benzamidine · ligand · chains A

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	240	0.66	0.83	35	empty
2	110	0.46	0.79	18	empty
3	56	0.31	0.75	12	empty
4	51	0.26	0.73	16	empty

Modifications

Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

2Y8D · Structure of DBL6 epsilon domain from VAR2CSA strain FCR3 · 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 2Y8D · PDBe 2Y8D · UniProt Q6UDW7

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