MolNFT v1 · #141524 · protein

Crystal structure of cona-R2M

5ZAC · Concanavalin-a: “Crystal structure of cona-R2M”. X-ray diffraction, 4 ligands (TA5, MAN, CA), 6 pockets (best druggability 0.83). MolNFT v1 #141524 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZAC
Type: protein
Length: 924 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-a
UniProt: P02866
Ligands: TA5, MAN, CA, MN
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Concanavalin-a	protein	230	4% helix, 45% strand	P02866
B	Concanavalin-a	protein	232	4% helix, 46% strand	P02866
C, D	Concanavalin-a	protein	231	5% helix, 44% strand	P02866

Ligands and binding sites

TA5 · 2H-1,2,3-triazol-4-ylmethanol · ligand · 2 copies · chains C, D
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains C, D
CA · Calcium ion · metal · 6 copies · chains A, B, C, D
MN · Manganese (II) 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

6 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	961	0.83	0.85	96	empty
2	128	0.78	0.96	24	empty
3	52	0.68	0.97	22	empty
4	157	0.49	0.78	27	CA
5	53	0.33	0.78	23	empty

Interfaces

4 interfaces between chains.

B–D · 1112 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1096 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 812 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 731 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5ZAC · Crystal structure of ConA-R2M · the same entry in another collection · chain D against D, TM-score 1.00
P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain C against A, TM-score 0.52

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 5ZAC · PDBe 5ZAC · UniProt P02866

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