MolNFT v1 · #7917 · protein

Nidogen-1 G2/PERLECAN IG3 complex

1GL4: “Nidogen-1 G2/PERLECAN IG3 complex”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.62). MolNFT v1 #7917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1GL4
Type: protein
Length: 362 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nidogen-1; Basement membrane-specific heparan sulfate proteoglycan core protein
UniProt: P10493, Q05793
Ligands: ZN
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nidogen-1	protein	273	10% helix, 52% strand	P10493
B	Basement membrane-specific heparan sulfate proteoglycan core protein	protein	89	7% helix, 57% strand	Q05793

Ligands and binding sites

ZN · Zinc ion · metal · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B

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

Pockets

2 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	297	0.62	0.79	30	empty
2	128	0.50	0.80	26	empty

Interfaces

1 interface between chains.

A–B · 1044 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1GL4 · Nidogen-1 G2/Perlecan IG3 Complex · the same entry in another collection · chain A against A, TM-score 1.00
P10493 · AlphaFold monomer V2.0 prediction for nidogen-1 (P10493) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P10493
Every structure of UniProt Q05793
Elsewhere: RCSB PDB 1GL4 · PDBe 1GL4 · UniProt P10493 · UniProt Q05793

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