MolNFT v1 · #19305 · protein

Room temperature structure of concanavalin a complexed to bivalent ligand

1QGL · Protein (succinylated concanavalin a ): “Room temperature structure of concanavalin a complexed to bivalent ligand”. X-ray diffraction, 3 ligands (EJT, MN, CA), 2 pockets (best druggability 0.38). MolNFT v1 #19305 on GenesisL1: 3D…

PDB: 1QGL
Type: protein
Length: 474 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (succinylated concanavalin a )
UniProt: P81461
Ligands: EJT, MN, CA
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein (succinylated concanavalin a )	protein	237	5% helix, 47% strand	P81461

Ligands and binding sites

EJT · 1,3-di(n-propyloxy-A-mannopyranosyl)-carbomyl 5-methyazido-benzene · ligand · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
SIN · Succinic acid · additive · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	70	0.38	0.79	17	empty
2	93	0.36	0.75	18	SIN

Interfaces

1 interface between chains.

A–B · 335 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

1QGL · Room temperature structure of concanavalin A complexed to bivalent ligand · the same entry in another collection · chain A against A, TM-score 1.00
P81461 · AlphaFold monomer V2.0 prediction for concanavalin-a (P81461) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P81461
Elsewhere: RCSB PDB 1QGL · PDBe 1QGL · UniProt P81461

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