MolNFT v1 · #165795 · protein

Neuronal growth regulator 1 (NEGR1)

6U6T: “Neuronal growth regulator 1 (NEGR1)”. X-ray diffraction, 4 ligands (NAG, BMA, FUC), 2 pockets (best druggability 0.38). MolNFT v1 #165795 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6U6T
Type: protein
Length: 539 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuronal growth regulator 1
UniProt: Q7Z3B1
Ligands: NAG, BMA, FUC, CA
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuronal growth regulator 1	protein	268	3% helix, 55% strand	Q7Z3B1
B	Neuronal growth regulator 1	protein	271	3% helix, 56% strand	Q7Z3B1

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies
FUC · alpha-L-fucopyranose · sugar · chains A
CA · Calcium ion · metal · 2 copies · chains A

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

Pockets

2 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	89	0.38	0.76	18	empty
2	56	0.28	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 1239 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6U6T · Neuronal growth regulator 1 (NEGR1) · the same entry in another collection · chain A against A, TM-score 1.00
Q7Z3B1 · AlphaFold monomer V2.0 prediction for neuronal growth regulator 1 (Q7Z3B1) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q7Z3B1
Elsewhere: RCSB PDB 6U6T · PDBe 6U6T · UniProt Q7Z3B1

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