MolNFT v1 · #18961 · protein
S-S-lambda-shaped trans and cis interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D MAP of desmosomes obtained by electron tomography
1Q5C · Ep-cadherin: “S-S-lambda-shaped trans and cis interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D MAP…”. Electron microscopy, 3 ligands (NAG, NDG, CA), 5 pockets (best druggability 0.78). MolNFT v1 #18961 on…
- PDB
- 1Q5C
- Type
- protein
- Length
- 2,160 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ep-cadherin
- Ligands
- NAG, NDG, CA
- Pockets
- 5 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 1% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ep-cadherin | protein | 540 | 1% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 52 copies · chains A, B, C, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 48 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.78 | 0.91 | 44 | empty |
| 2 | 187 | 0.58 | 0.81 | 26 | empty |
| 3 | 50 | 0.37 | 0.80 | 18 | empty |
| 4 | 100 | 0.36 | 0.74 | 15 | empty |
| 5 | 52 | 0.27 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1464 Ų buried · 115 hydrogen bonds · protein-protein
- A–B · 1009 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 655 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 646 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 645 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 glycan, 8 disulfide, 1 isopeptide (O-glycosylation, N-glycosylation, disulfide, isopeptide).
Compared structures
- 1Q5C · S-S-lambda-shaped TRANS and CIS interactions of cadherins model based on fitting… · 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 1Q5C · PDBe 1Q5C
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