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Three dimensional structure of the giant reed (arundodonax) lectin (adl) complex with sialic acid

Analyse Three dimensional structure of the giant reed (arundodonax) lectin (adl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6STP
Type: protein
Length: 330 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arundo donax lectin (adl)
Ligands: SIA
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Arundo donax lectin (adl)	protein	165	20% helix, 19% strand	—

Ligands and binding sites

SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	137	0.62	0.86	36	empty
2	117	0.58	0.85	32	empty
3	70	0.38	0.79	21	empty
4	67	0.35	0.77	21	empty

Interfaces

1 interface between chains.

A–B · 2249 Å² buried · 43 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide (disulfide).

Compared structures

6STP · Three dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with… · 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 6STP · PDBe 6STP

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