Research workbench
Complex between transferrin receptor 1 and transferrin with iron in the N-lobe, cryocooled 1
Analyse Complex between transferrin receptor 1 and transferrin with iron in the N-lobe… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S9M
- Type
- protein
- Length
- 2,282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferrin receptor protein 1; Serotransferrin
- UniProt
- P02786, P02787
- Ligands
- NAG, CA, FE, CO3
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transferrin receptor protein 1 | protein | 638 | 38% helix, 18% strand | P02786 |
| B | Transferrin receptor protein 1 | protein | 639 | 38% helix, 17% strand | P02786 |
| C | Serotransferrin | protein | 517 | 33% helix, 19% strand | P02787 |
| D | Serotransferrin | protein | 488 | 33% helix, 15% strand | P02787 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains C, D
- CO3 · Carbonate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.85 | 0.89 | 86 | empty |
| 2 | 213 | 0.79 | 0.93 | 40 | empty |
| 3 | 707 | 0.78 | 0.83 | 67 | empty |
| 4 | 820 | 0.78 | 0.81 | 71 | empty |
| 5 | 1200 | 0.76 | 0.79 | 113 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1308 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1212 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 531 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 451 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3S9M · Complex between transferrin receptor 1 and transferrin with iron in the N-Lobe… · the same entry in another collection · chain D against D, 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 0.99
- P02787 · AlphaFold monomer V2.0 prediction for serotransferrin (P02787) · a predicted model of the same protein · chain D 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
- Every structure of UniProt P02787
- Elsewhere: RCSB PDB 3S9M · PDBe 3S9M · UniProt P02786 · UniProt P02787
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