MolNFT v1 · #103218 · protein

Structure of CONA/RH3MAN

4P9W · Concanavalin-a: “Structure of CONA/RH3MAN”. X-ray diffraction, 3 ligands (R3M, MN, CA), 3 pockets (best druggability 0.87). MolNFT v1 #103218 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4P9W
Type: protein
Length: 948 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-a
UniProt: P02866
Ligands: R3M, MN, CA
Pockets: 3 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Concanavalin-a	protein	237	4% helix, 47% strand	P02866

Ligands and binding sites

R3M · 2-[2-(2-{4-[(alpha-D-mannopyranosyloxy)methyl]-1H-1,2, 3-triazol-1-yl}ethoxy)ethoxy]ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate · ligand · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	968	0.87	0.88	113	empty
2	63	0.40	0.80	20	empty
3	55	0.28	0.74	19	empty

Interfaces

5 interfaces between chains.

A–B · 1203 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1192 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 1148 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1105 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 11 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4P9W · Structure of ConA/Rh3Man · the same entry in another collection · chain A against A, TM-score 1.00
P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain A against A, TM-score 0.50

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 P02866
Elsewhere: RCSB PDB 4P9W · PDBe 4P9W · UniProt P02866

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