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Lectin from bauhinia forficata in complex with tn-peptide

Analyse Lectin from bauhinia forficata in complex with tn-peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5T5P
Type: protein
Length: 464 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin; Tn antigen ACE-ser-thr-val-gly
UniProt: P86993
Ligands: ACE, A2G, CA, CL
Pockets: 6 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lectin	protein	229	7% helix, 49% strand	P86993
a, b	Tn antigen ACE-ser-thr-val-gly	protein	3	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, a, B, b
A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, a, B, b
CA · Calcium ion · metal · 4 copies · chains A, B
CL · Chloride ion · ion · chains B
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	104	0.45	0.79	22	EDO
2	89	0.44	0.80	19	A2G
3	123	0.44	0.77	22	EDO
4	88	0.43	0.79	19	A2G
5	60	0.42	0.82	16	empty

Interfaces

3 interfaces between chains.

A–B · 856 Å² buried · 17 hydrogen bonds · protein-protein
A–a · 147 Å² buried · 2 hydrogen bonds · protein-protein
B–b · 138 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 glycan (covalent ligand, O-glycosylation).

Compared structures

5T5P · Lectin from bauhinia forficata in complex with tn-peptide · the same entry in another collection · chain A against A, TM-score 1.00
P86993 · AlphaFold monomer V2.0 prediction for lectin (P86993) · 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 P86993
Elsewhere: RCSB PDB 5T5P · PDBe 5T5P · UniProt P86993

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