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Crystal structure of the psathyrella asperospora lectin pal in complex with glcnac

Analyse Crystal structure of the psathyrella asperospora lectin pal in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MB4
Type: protein
Length: 401 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glcnac specific lectin
Ligands: NAG, NDG, NA
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glcnac specific lectin	protein	401	3% helix, 37% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A
NA · Sodium ion · metal · 6 copies · chains A
MLI · Malonate ion · additive · chains A

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

Pockets

3 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	1062	0.79	0.80	63	empty
2	249	0.56	0.78	32	empty
3	97	0.48	0.80	17	empty

Compared structures

5MB4 · Crystal Structure of the Psathyrella asperospora lectin PAL in complex with GlcNAc · 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
Elsewhere: RCSB PDB 5MB4 · PDBe 5MB4

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