MolNFT v1 · #103219 · protein

Structure of CONA/RH3GLU complex

4P9X · Concanavalin-a: “Structure of CONA/RH3GLU complex”. X-ray diffraction, 3 ligands (R3G, MN, CA), 7 pockets (best druggability 0.83). MolNFT v1 #103219 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4P9X
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: R3G, MN, CA
Pockets: 7 · best druggability 0.83

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Concanavalin-a	protein	237	5% helix, 46% strand	P02866

Ligands and binding sites

R3G · 2-[2-(2-{4-[(alpha-D-glucopyranosyloxy)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

7 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	1100	0.83	0.85	129	empty
2	140	0.77	0.95	26	empty
3	69	0.63	0.92	28	empty
4	54	0.31	0.76	18	empty
5	65	0.31	0.75	17	empty

Interfaces

4 interfaces between chains.

A–B · 1230 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1221 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1141 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 1133 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4P9X · Structure of ConA/Rh3Glu complex · 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 4P9X · PDBe 4P9X · UniProt P02866

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