Research workbench
Crystal structure of mouse nectin-like molecule 4 (mnecl-4) full ectodomain in complex with mouse nectin-like molecule 1 (mnecl-1) IG1 domain, 3.3A
Analyse Crystal structure of mouse nectin-like molecule 4 (mnecl-4) full ectodomain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZO2
- Type
- protein
- Length
- 589 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell adhesion molecule 4; Cell adhesion molecule 3
- UniProt
- Q8R464, Q99N28
- Ligands
- NAG, FUC
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell adhesion molecule 4 | protein | 196 | 2% helix, 51% strand | Q8R464 |
| C | Cell adhesion molecule 4 | protein | 293 | 2% helix, 55% strand | Q8R464 |
| B | Cell adhesion molecule 3 | protein | 100 | 3% helix, 51% strand | Q99N28 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
- FUC · alpha-L-fucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.61 | 0.77 | 41 | empty |
| 2 | 94 | 0.44 | 0.80 | 22 | empty |
| 3 | 85 | 0.43 | 0.79 | 22 | empty |
Interfaces
2 interfaces between chains.
- C–B · 774 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 545 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5ZO2 · Crystal structure of mouse nectin-like molecule 4 (mNecl-4) full ectodomain in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q99N28 · AlphaFold monomer V2.0 prediction for cell adhesion molecule 3 (Q99N28) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q8R464 · AlphaFold monomer V2.0 prediction for cell adhesion molecule 4 (Q8R464) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8R464
- Every structure of UniProt Q99N28
- Elsewhere: RCSB PDB 5ZO2 · PDBe 5ZO2 · UniProt Q8R464 · UniProt Q99N28
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.