MolNFT v1 · #134488 · protein

Lectin from bauhinia forficata in complex with tn-peptide

5T5L: “Lectin from bauhinia forficata in complex with tn-peptide”. X-ray diffraction, 4 ligands (ACE, A2G, CA), 6 pockets (best druggability 0.47). MolNFT v1 #134488 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5T5L
Type: protein
Length: 465 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin; Tn antigen ACE-ser-ser-val-gly
UniProt: P86993
Ligands: ACE, A2G, CA, CL
Pockets: 6 · best druggability 0.47

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lectin	protein	229	6% helix, 49% strand	P86993
a	Tn antigen ACE-ser-ser-val-gly	protein	3	0% helix, 0% strand	—
b	Tn antigen ACE-ser-ser-val-gly	protein	4	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 · 10 copies · chains A, B
GOL · Glycerol · additive · chains 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	91	0.47	0.81	19	A2G
2	107	0.45	0.79	22	EDO
3	89	0.45	0.80	20	A2G
4	99	0.44	0.79	19	EDO
5	172	0.39	0.72	41	empty

Interfaces

3 interfaces between chains.

A–B · 852 Å² buried · 17 hydrogen bonds · protein-protein
A–a · 131 Å² buried · 2 hydrogen bonds · protein-protein
B–b · 117 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5T5L · 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 5T5L · PDBe 5T5L · UniProt P86993

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