Research workbench

MAN(APLHA1-6)MAN(ALPHA1-O)METHYL concanavalin a complex

Analyse MAN(APLHA1-6)MAN(ALPHA1-O)METHYL concanavalin a complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QDC
Type: protein
Length: 948 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (concanavalin a)
UniProt: P55915
Ligands: MMA, MAN, MN, CA, CL
Pockets: 4 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protein (concanavalin a)	protein	237	5% helix, 46% strand	P55915

Ligands and binding sites

MMA · methyl alpha-D-mannopyranoside · sugar · 4 copies · chains A, B, C, D
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 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	459	0.80	0.88	76	empty
2	292	0.76	0.89	46	empty
3	64	0.38	0.79	21	empty
4	50	0.35	0.79	17	empty

Interfaces

4 interfaces between chains.

A–B · 1204 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1193 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1104 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1099 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1QDC · MAN(APLHA1-6)MAN(ALPHA1-O)METHYL concanavalin a complex · the same entry in another collection · chain D against D, TM-score 1.00
P55915 · AlphaFold monomer V2.0 prediction for concanavalin-br (P55915) · a predicted model of the same protein · chain C 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 P55915
Elsewhere: RCSB PDB 1QDC · PDBe 1QDC · UniProt P55915

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