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Crystal structure of basic winged bean lectin with tn-antigen

Analyse Crystal structure of basic winged bean lectin with tn-antigen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2D3S
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: SER, NAG, FUC, A2G, BMA, CA, MN
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Basic agglutinin	protein	237	4% helix, 46% strand	O24313

Ligands and binding sites

SER · Serine · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
FUC · alpha-L-fucopyranose · sugar · 6 copies
A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar
CA · Calcium ion · metal · 4 copies · chains A, B, C, D
MN · Manganese (II) 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

7 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	687	0.75	0.80	77	empty
2	67	0.40	0.80	17	empty
3	64	0.35	0.77	18	A2G
4	76	0.34	0.75	16	empty
5	68	0.31	0.74	15	empty

Interfaces

5 interfaces between chains.

C–D · 834 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 825 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 289 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 286 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 39 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 glycan (N-glycosylation).

Compared structures

2D3S · Crystal Structure of basic winged bean lectin with Tn-antigen · the same entry in another collection · chain D against D, TM-score 1.00
O24313 · AlphaFold monomer V2.0 prediction for basic agglutinin (O24313) · a predicted model of the same protein · chain D 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 2D3S · PDBe 2D3S · UniProt O24313

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