Research workbench
Trypanosoma brucei transferrin receptor in complex with human transferrin
Analyse Trypanosoma brucei transferrin receptor in complex with human transferrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SOY
- Type
- protein
- Length
- 1,288 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ESAG6, subunit of heterodimeric transferrin receptor; ESAG7, subunit of heterodimeric…
- UniProt
- Q8WPU1, Q8WPU2, P02787
- Ligands
- NAG, FE
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ESAG6, subunit of heterodimeric transferrin receptor | protein | 323 | 57% helix, 8% strand | Q8WPU1 |
| B | ESAG7, subunit of heterodimeric transferrin receptor | protein | 313 | 54% helix, 8% strand | Q8WPU2 |
| C | Serotransferrin | protein | 652 | 38% helix, 19% strand | P02787 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- FE · Fe (III) ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.81 | 0.87 | 47 | empty |
| 2 | 1049 | 0.81 | 0.83 | 101 | empty |
| 3 | 114 | 0.77 | 0.97 | 26 | empty |
| 4 | 52 | 0.70 | 0.97 | 11 | empty |
| 5 | 298 | 0.69 | 0.83 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4150 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 775 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6SOY · Trypanosoma brucei transferrin receptor in complex with human transferrin · the same entry in another collection · chain C against C, TM-score 1.00
- P02787 · AlphaFold monomer V2.0 prediction for serotransferrin (P02787) · a predicted model of the same protein · chain C against A, TM-score 0.84
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 Q8WPU1
- Every structure of UniProt Q8WPU2
- Every structure of UniProt P02787
- Elsewhere: RCSB PDB 6SOY · PDBe 6SOY · UniProt Q8WPU1 · UniProt Q8WPU2 · UniProt P02787
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