Research workbench

Concanavalin a-hexapeptide complex

Analyse Concanavalin a-hexapeptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JOJ
Type: protein
Length: 972 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-br; Hexapeptide
UniProt: P55915
Ligands: ACE, MN, CA, NH2
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Concanavalin-br	protein	237	3% helix, 51% strand	P55915
P, Q, R, S	Hexapeptide	protein	6	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 4 copies · chains A, P, B, Q, C, R, S
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D
NH2 · Amino group · ion · 4 copies · chains A, P, Q, R, S

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	54	0.72	0.99	17	empty
2	66	0.71	0.97	25	empty
3	50	0.67	0.97	21	empty

Interfaces

6 interfaces between chains.

C–D · 1209 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1188 Å² buried · 24 hydrogen bonds · protein-protein
A–P · 402 Å² buried · 9 hydrogen bonds · protein-protein
D–S · 363 Å² buried · 4 hydrogen bonds · protein-protein
C–R · 362 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

1JOJ · Concanavalin a-hexapeptide 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 1JOJ · PDBe 1JOJ · UniProt P55915

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