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1.8A crystal structure of of psathyrella velutina lectin in complex with methyl 2-acetamido-1,2-dideoxy-1-seleno-beta-D-glucopyranoside

Analyse 1.8A crystal structure of of psathyrella velutina lectin in complex with methyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BWM
Type: protein
Length: 400 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Psathyrella velutina lectin pvl
Ligands: SNG, CA, SO4
Pockets: 2 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Psathyrella velutina lectin pvl	protein	400	3% helix, 38% strand	—

Ligands and binding sites

SNG · methyl 2-acetamido-2-deoxy-1-seleno-beta-D-glucopyranoside · ligand · 5 copies · chains A
CA · Calcium ion · metal · 2 copies · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A
GOL · Glycerol · additive · chains A

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	1061	0.79	0.81	67	empty
2	326	0.64	0.80	31	empty

Compared structures

2BWM · 1.8A CRYSTAL STRUCTURE OF of Psathyrella velutina LECTIN IN COMPLEX WITH METHYL… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 2BWM · PDBe 2BWM

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