MolNFT v1 · #141383 · protein

Crystal structure of cona-R1M

5Z5N · Concanavalin-a: “Crystal structure of cona-R1M”. X-ray diffraction, 3 ligands (MAN, CA, MN), 4 pockets (best druggability 0.85). MolNFT v1 #141383 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Z5N
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: MAN, CA, MN
Pockets: 4 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Concanavalin-a	protein	231	4% helix, 46% strand	P02866
C	Concanavalin-a	protein	233	5% helix, 44% strand	P02866
D	Concanavalin-a	protein	229	5% helix, 45% strand	P02866

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · chains B
CA · Calcium ion · metal · 4 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

4 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	995	0.85	0.86	119	empty
2	53	0.41	0.82	11	empty
3	50	0.30	0.77	21	empty
4	59	0.30	0.75	18	empty

Interfaces

4 interfaces between chains.

C–D · 1073 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1039 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 719 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 649 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5Z5N · Crystal structure of ConA-R1M · 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 B against A, TM-score 0.51

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 5Z5N · PDBe 5Z5N · UniProt P02866

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.