MolNFT v1 · #56668 · protein

Crystl structure of basic winged bean lectin in complex with gal- alpha-1,4-gal-beta-ethylene

2ZMK · Basic agglutinin: “Crystl structure of basic winged bean lectin in complex with gal- alpha-1,4-gal-beta-ethylene”. X-ray diffraction, 7 ligands (EGA, NAG, FUC), 6 pockets (best druggability 0.76). MolNFT v1 #56668 on GenesisL1: 3D…

PDB: 2ZMK
Type: protein
Length: 948 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Basic agglutinin
UniProt: O24313
Ligands: EGA, NAG, FUC, GLA, BMA, MN, CA
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Basic agglutinin	protein	237	4% helix, 45% strand	O24313

Ligands and binding sites

EGA · ethyl beta-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C, D
FUC · alpha-L-fucopyranose · sugar · 6 copies
GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar
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

6 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	831	0.76	0.80	101	empty
2	69	0.31	0.74	18	empty
3	57	0.31	0.76	18	GLA
4	62	0.30	0.74	16	empty
5	54	0.29	0.76	17	empty

Interfaces

5 interfaces between chains.

A–B · 849 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 843 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 299 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 294 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 46 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan (N-glycosylation).

Compared structures

2ZMK · Crystl structure of Basic Winged bean lectin in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
O24313 · AlphaFold monomer V2.0 prediction for basic agglutinin (O24313) · 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 O24313
Elsewhere: RCSB PDB 2ZMK · PDBe 2ZMK · UniProt O24313

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