MolNFT v1 · #11838 · protein

Concanavalin A/12-mer peptide complex

1JYI · Concanavalin-br: “Concanavalin A/12-mer peptide complex”. X-ray diffraction, 2 ligands (MN, CA), 2 pockets (best druggability 0.71). MolNFT v1 #11838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JYI
Type: protein
Length: 996 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-br; 12-mer peptide
UniProt: P55915
Ligands: MN, CA
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Concanavalin-br	protein	237	4% helix, 51% strand	P55915
P, Q, R, S	12-mer peptide	protein	12	0% helix, 0% strand	—

Ligands and binding sites

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

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	67	0.71	0.97	22	empty
2	55	0.26	0.73	19	empty

Interfaces

6 interfaces between chains.

C–D · 1182 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1173 Å² buried · 19 hydrogen bonds · protein-protein
D–S · 586 Å² buried · 7 hydrogen bonds · protein-protein
A–P · 575 Å² buried · 10 hydrogen bonds · protein-protein
C–R · 363 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1JYI · Concanavalin A/12-mer peptide complex · the same entry in another collection · chain S against S, TM-score 1.00
P55915 · AlphaFold monomer V2.0 prediction for concanavalin-br (P55915) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P55915
Elsewhere: RCSB PDB 1JYI · PDBe 1JYI · UniProt P55915

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