MolNFT v1 · #19228 · protein

MAN(APLHA1-3)MAN(ALPHA1-O)METHYL concanavalin a complex

1QDO · Protein (concanavalin a): “MAN(APLHA1-3)MAN(ALPHA1-O)METHYL concanavalin a complex”. X-ray diffraction, 4 ligands (MMA, MAN, MN), 3 pockets (best druggability 0.83). MolNFT v1 #19228 on GenesisL1: 3D structure, binding sites and…

PDB: 1QDO
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
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protein (concanavalin a)	protein	237	4% 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

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	820	0.83	0.86	113	empty
2	132	0.78	0.96	25	empty
3	125	0.75	0.94	27	empty

Interfaces

5 interfaces between chains.

A–B · 1232 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1222 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1094 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 1086 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 11 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1QDO · MAN(APLHA1-3)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 D 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 1QDO · PDBe 1QDO · UniProt P55915

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