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Crystal structure of cona-R3M

Analyse Crystal structure of cona-R3M in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z5P
Type: protein
Length: 443 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-a
UniProt: P02866
Ligands: R3M, CA, MN
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Concanavalin-a	protein	220	4% helix, 45% strand	P02866
B	Concanavalin-a	protein	223	6% helix, 46% 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 · 2 copies · chains A, B
CA · Calcium ion · metal · 3 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.62	0.83	24	empty
2	61	0.28	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 377 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5Z5P · Crystal structure of ConA-R3M · 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 0.53

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 5Z5P · PDBe 5Z5P · UniProt P02866

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