Research workbench
Crystal structure of TFR1 mimicry in complex with GP1 from macv
Analyse Crystal structure of TFR1 mimicry in complex with GP1 from macv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S9J
- Type
- protein
- Length
- 1,208 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-glycoprotein polyprotein gp complex; Transferrin receptor 1,TRANSFERRIN receptor 1
- UniProt
- Q8AZ57, A0A060BIS8
- Ligands
- NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pre-glycoprotein polyprotein gp complex | protein | 155 | 26% helix, 23% strand | Q8AZ57 |
| A | Transferrin receptor 1,TRANSFERRIN receptor 1 | protein | 151 | 18% helix, 30% strand | A0A060BIS8 |
| D | Pre-glycoprotein polyprotein gp complex | protein | 152 | 27% helix, 24% strand | Q8AZ57 |
| C, E, G | Transferrin receptor 1,TRANSFERRIN receptor 1 | protein | 149 | 18% helix, 31% strand | A0A060BIS8 |
| F | Pre-glycoprotein polyprotein gp complex | protein | 149 | 28% helix, 22% strand | Q8AZ57 |
| H | Pre-glycoprotein polyprotein gp complex | protein | 154 | 25% helix, 22% strand | Q8AZ57 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, A, D, C
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.65 | 0.77 | 61 | empty |
| 2 | 470 | 0.65 | 0.77 | 45 | NAG |
| 3 | 318 | 0.64 | 0.80 | 41 | empty |
| 4 | 248 | 0.61 | 0.80 | 36 | empty |
| 5 | 301 | 0.57 | 0.77 | 39 | NAG |
Interfaces
8 interfaces between chains.
- H–G · 1082 Ų buried · 17 hydrogen bonds · protein-protein
- F–E · 1080 Ų buried · 19 hydrogen bonds · protein-protein
- B–A · 1066 Ų buried · 20 hydrogen bonds · protein-protein
- D–C · 1064 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 617 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6S9J · Crystal structure of TfR1 mimicry in complex with GP1 from MACV · the same entry in another collection · chain B against B, 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 Q8AZ57
- Every structure of UniProt A0A060BIS8
- Elsewhere: RCSB PDB 6S9J · PDBe 6S9J · UniProt Q8AZ57 · UniProt A0A060BIS8
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