Research workbench

Structure of colocasia esculenta agglutinin

Analyse Structure of colocasia esculenta agglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5D5G
Type: protein
Length: 439 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tuber agglutinin
UniProt: R9RL27
Ligands: MG, SO4
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Tuber agglutinin	protein	109	0% helix, 45% strand	R9RL27
B	Tuber agglutinin	protein	110	0% helix, 42% strand	R9RL27
D	Tuber agglutinin	protein	111	0% helix, 38% strand	R9RL27

Ligands and binding sites

MG · Magnesium ion · metal · 5 copies · chains A, B
SO4 · Sulfate ion · ion · chains B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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	486	0.76	0.85	65	empty
2	52	0.31	0.77	15	empty

Interfaces

5 interfaces between chains.

C–D · 1864 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1702 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 337 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 215 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 195 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5D5G · Structure of colocasia esculenta agglutinin · the same entry in another collection · chain D against D, TM-score 1.00
R9RL27 · AlphaFold monomer V2.0 prediction for mannose-specific lectin cea (R9RL27) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 R9RL27
Elsewhere: RCSB PDB 5D5G · PDBe 5D5G · UniProt R9RL27

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