Research workbench
Crystal structure of NIDOGEN/LAMININ complex
Analyse Crystal structure of NIDOGEN/LAMININ complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NPE
- Type
- protein
- Length
- 427 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nidogen; Laminin gamma-1 chain
- UniProt
- P02468, P10493
- Ligands
- CD
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nidogen | protein | 263 | 1% helix, 58% strand | P02468 |
| B | Laminin gamma-1 chain | protein | 164 | 4% helix, 25% strand | P10493 |
Ligands and binding sites
- CD · Cadmium ion · metal · 6 copies · chains A, B
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.77 | 0.86 | 46 | empty |
| 2 | 124 | 0.43 | 0.76 | 27 | empty |
| 3 | 131 | 0.42 | 0.76 | 20 | empty |
| 4 | 113 | 0.41 | 0.77 | 19 | CD |
| 5 | 90 | 0.40 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 892 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1NPE · Crystal structure of Nidogen/Laminin 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 B against A, TM-score 0.36
- P02468 · AlphaFold monomer V2.0 prediction for laminin subunit gamma-1 (P02468) · a predicted model of the same protein · chain A against A, TM-score 0.27
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 P02468
- Every structure of UniProt P10493
- Elsewhere: RCSB PDB 1NPE · PDBe 1NPE · UniProt P02468 · UniProt P10493
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