MolNFT v1 · #105496 · protein

Jacalin-carbohydrate interactions. distortion of the ligand as a determinant of affinity

4R6N · Agglutinin alpha chain: “Jacalin-carbohydrate interactions. distortion of the ligand as a determinant of affinity”. X-ray diffraction, 1 ligand (MBG), 5 pockets (best druggability 0.83). MolNFT v1 #105496 on GenesisL1: 3D structure…

PDB: 4R6N
Type: protein
Length: 595 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agglutinin alpha chain; Agglutinin beta-3 chain
UniProt: P18670, P18673
Ligands: MBG
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Agglutinin alpha chain	protein	133	0% helix, 67% strand	P18670
B, D, F	Agglutinin beta-3 chain	protein	16	0% helix, 44% strand	P18673
H	Agglutinin beta-3 chain	protein	15	0% helix, 47% strand	P18673

Ligands and binding sites

MBG · methyl beta-D-galactopyranoside · ligand · 3 copies · chains A, E, G
IPA · Isopropyl alcohol · additive · 18 copies · chains A, E, C, B, H, G, D
EDO · 1,2-ethanediol · additive · 5 copies · chains A, F, C, D, E, G, H

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

Pockets

5 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	478	0.83	0.90	68	IPA
2	84	0.35	0.75	19	empty
3	100	0.34	0.73	27	empty
4	73	0.31	0.74	16	EDO
5	59	0.30	0.75	18	empty

Interfaces

22 interfaces between chains.

E–F · 565 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 549 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 541 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 533 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 444 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4R6N · Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity · the same entry in another collection · chain H against H, TM-score 1.00
P18670 · AlphaFold monomer V2.0 prediction for agglutinin alpha chain (P18670) · a predicted model of the same protein · chain A against A, TM-score 1.00
P18673 · AlphaFold monomer V2.0 prediction for agglutinin beta-3 chain (P18673) · a predicted model of the same protein · chain B against A, TM-score 0.33

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 P18670
Every structure of UniProt P18673
Elsewhere: RCSB PDB 4R6N · PDBe 4R6N · UniProt P18670 · UniProt P18673

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