Research workbench
Lambda-shaped trans and cis interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D MAP of desmosomes obtained by electron tomography
Analyse Lambda-shaped trans and cis interactions of cadherins model based on fitting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q5B
- Type
- protein
- Length
- 1,620 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ep-cadherin
- Ligands
- NAG, NDG, CA
- Pockets
- 6 · best druggability 0.69
Structure
electron microscopy · 1 distinct chain · 1% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ep-cadherin | protein | 540 | 1% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C
- CA · Calcium ion · metal · 36 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.69 | 0.91 | 35 | empty |
| 2 | 59 | 0.58 | 0.89 | 26 | empty |
| 3 | 142 | 0.56 | 0.82 | 31 | empty |
| 4 | 150 | 0.54 | 0.81 | 29 | empty |
| 5 | 138 | 0.51 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 851 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 777 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 673 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 6 disulfide (O-glycosylation, N-glycosylation, disulfide).
Compared structures
- 1Q5B · lambda-shaped TRANS and CIS interactions of cadherins model based on fitting C-cadherin… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 1Q5B · PDBe 1Q5B
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