Research workbench
Crystal structure of the ectodomain of human transferrin receptor
Analyse Crystal structure of the ectodomain of human transferrin receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CX8
- Type
- protein
- Length
- 5,112 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferrin receptor protein
- UniProt
- P02786
- Ligands
- NAG, SM
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Transferrin receptor protein | protein | 639 | 36% helix, 15% strand | P02786 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, C, D, E, F, G, H
- SM · Samarium (III) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.85 | 0.86 | 112 | empty |
| 2 | 769 | 0.84 | 0.87 | 88 | SM |
| 3 | 983 | 0.84 | 0.85 | 85 | empty |
| 4 | 604 | 0.83 | 0.88 | 61 | SM |
| 5 | 690 | 0.82 | 0.86 | 75 | SM |
Interfaces
7 interfaces between chains.
- A–B · 3032 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 3012 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 2983 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 2975 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 2851 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 16 disulfide (N-glycosylation, disulfide).
Compared structures
- 1CX8 · Crystal structure of the ectodomain of human transferrin receptor · the same entry in another collection · chain H against H, TM-score 1.00
- P02786 · AlphaFold monomer V2.0 prediction for transferrin receptor protein 1 (P02786) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P02786
- Elsewhere: RCSB PDB 1CX8 · PDBe 1CX8 · UniProt P02786
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.