Research workbench
Nidogen-1 G2/PERLECAN IG3 complex
Analyse Nidogen-1 G2/PERLECAN IG3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.