Research workbench
Zebrafish ret cadherin like domains 1 to 4.
Analyse Zebrafish ret cadherin like domains 1 to 4. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AMK
- Type
- protein
- Length
- 948 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase receptor ret
- EC
- 2.7.10.1
- UniProt
- A8E7C6
- Ligands
- NAG, FUC, MAN, BMA, CA
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 476 | 12% helix, 43% strand | A8E7C6 |
| B | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 472 | 11% helix, 44% strand | A8E7C6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 4 copies
- CA · Calcium ion · metal · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B
- PGE · Triethylene glycol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.78 | 0.83 | 74 | PGE |
| 2 | 784 | 0.76 | 0.80 | 85 | empty |
| 3 | 119 | 0.74 | 0.93 | 23 | GOL |
| 4 | 592 | 0.72 | 0.80 | 71 | GOL, PGE, PEG |
| 5 | 557 | 0.69 | 0.79 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 1957 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 9 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7AMK · Zebrafish RET Cadherin Like Domains 1 to 4. · 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
- Every structure of UniProt A8E7C6
- Elsewhere: RCSB PDB 7AMK · PDBe 7AMK · UniProt A8E7C6
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