MolNFT v1 · #4134 · protein
Hemochromatosis protein hfe complexed with transferrin receptor
1DE4: “Hemochromatosis protein hfe complexed with transferrin receptor”. X-ray diffraction, 2 ligands (NAG, CA), 20 pockets (best druggability 0.86). MolNFT v1 #4134 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1DE4
- Type
- protein
- Length
- 3,018 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemochromatosis protein; Beta-2-microglobulin; Transferrin receptor
- UniProt
- Q30201, P61769, P02786
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Hemochromatosis protein | protein | 272 | 28% helix, 39% strand | Q30201 |
| B, E, H | Beta-2-microglobulin | protein | 99 | 0% helix, 45% strand | P61769 |
| C, F, I | Transferrin receptor | protein | 635 | 39% helix, 18% strand | P02786 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, D, F, A, I
- CA · Calcium ion · metal · 3 copies · chains C, F, I
- GOL · Glycerol · additive · chains G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.86 | 0.96 | 75 | empty |
| 2 | 714 | 0.80 | 0.84 | 61 | empty |
| 3 | 1056 | 0.80 | 0.81 | 96 | empty |
| 4 | 702 | 0.79 | 0.83 | 49 | empty |
| 5 | 854 | 0.78 | 0.81 | 64 | empty |
Interfaces
10 interfaces between chains.
- C–F · 3075 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1335 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 1318 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1317 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1082 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1DE4 · Hemochromatosis protein hfe complexed with transferrin receptor · the same entry in another collection · chain I against I, TM-score 1.00
- P02786 · AlphaFold monomer V2.0 prediction for transferrin receptor protein 1 (P02786) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B 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 Q30201
- Every structure of UniProt P61769
- Every structure of UniProt P02786
- Elsewhere: RCSB PDB 1DE4 · PDBe 1DE4 · UniProt Q30201 · UniProt P61769 · UniProt P02786
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