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Concanavalin A/15-mer peptide complex

Analyse Concanavalin A/15-mer peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JYC
Type: protein
Length: 1,008 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-br; 15-mer peptide
UniProt: P55915
Ligands: MN, CA
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Concanavalin-br	protein	237	4% helix, 44% strand	P55915
P, Q, R, S	15-mer peptide	protein	15	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

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	54	0.71	0.98	17	empty
2	81	0.64	0.91	25	empty
3	53	0.34	0.78	16	empty

Interfaces

6 interfaces between chains.

A–B · 1178 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1161 Å² buried · 20 hydrogen bonds · protein-protein
A–P · 701 Å² buried · 12 hydrogen bonds · protein-protein
D–S · 693 Å² buried · 12 hydrogen bonds · protein-protein
C–R · 663 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1JYC · CONCANAVALIN A/15-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 C 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 1JYC · PDBe 1JYC · UniProt P55915

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