MolNFT v1 · #67391 · protein

Ligand-receptor structure

3IJ2 · Beta-nerve growth factor: “Ligand-receptor structure”. X-ray diffraction, 8 pockets (best druggability 0.72). MolNFT v1 #67391 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3IJ2
Type: protein
Length: 542 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-nerve growth factor; Nerve growth factor receptor (tnfr superfamily, member 16)
UniProt: P01139, P07174
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-nerve growth factor	protein	110	0% helix, 53% strand	P01139
X	Nerve growth factor receptor (tnfr superfamily, member 16)	protein	162	0% helix, 35% strand	P07174
Y	Nerve growth factor receptor (tnfr superfamily, member 16)	protein	160	0% helix, 32% strand	P07174

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	384	0.72	0.83	49	empty
2	778	0.71	0.77	55	empty
3	753	0.69	0.76	51	empty
4	420	0.64	0.78	51	empty
5	100	0.35	0.74	19	empty

Interfaces

6 interfaces between chains.

A–B · 1176 Å² buried · 10 hydrogen bonds · protein-protein
A–Y · 714 Å² buried · 4 hydrogen bonds · protein-protein
X–B · 685 Å² buried · 4 hydrogen bonds · protein-protein
B–Y · 636 Å² buried · 3 hydrogen bonds · protein-protein
A–X · 625 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 disulfide (disulfide).

Compared structures

3IJ2 · Ligand-receptor structure · the same entry in another collection · chain A against A, TM-score 1.00
P01139 · AlphaFold monomer V2.0 prediction for beta-nerve growth factor (P01139) · a predicted model of the same protein · chain A against A, TM-score 0.92
P07174 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain Y against A, TM-score 0.91

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 P01139
Every structure of UniProt P07174
Elsewhere: RCSB PDB 3IJ2 · PDBe 3IJ2 · UniProt P01139 · UniProt P07174

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