Research workbench
Glycosylated trypanosoma brucei transferrin receptor in complex with human transferrin
Analyse Glycosylated trypanosoma brucei transferrin receptor in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SOZ
- Type
- protein
- Length
- 1,294 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, MAN, FE
- Pockets
- 12 · best druggability 0.84
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 | 58% helix, 9% strand | Q8WPU1 |
| B | ESAG7, subunit of heterodimeric transferrin receptor | protein | 320 | 56% helix, 9% strand | Q8WPU2 |
| C | Serotransferrin | protein | 651 | 38% helix, 19% strand | P02787 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- FE · Fe (III) ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.84 | 0.85 | 95 | empty |
| 2 | 498 | 0.80 | 0.87 | 47 | empty |
| 3 | 542 | 0.78 | 0.85 | 78 | empty |
| 4 | 51 | 0.71 | 0.98 | 14 | empty |
| 5 | 169 | 0.54 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4262 Ų buried · 59 hydrogen bonds · protein-protein
- B–C · 786 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6SOZ · Glycosylated Trypanosoma brucei transferrin receptor in complex with human transferrin · 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 Q8WPU1
- Every structure of UniProt Q8WPU2
- Every structure of UniProt P02787
- Elsewhere: RCSB PDB 6SOZ · PDBe 6SOZ · UniProt Q8WPU1 · UniProt Q8WPU2 · UniProt P02787
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