Research workbench
Cryo-EM structure of human transferrin receptor 1 bound to DNA aptamer
Analyse Cryo-EM structure of human transferrin receptor 1 bound to DNA aptamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZQS
- Type
- protein + DNA
- Length
- 1,338 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (30-mer); Transferrin receptor protein 1
- UniProt
- P02786
- Ligands
- NAG, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA (30-mer) | dna | 30 | — | — |
| B, D | Transferrin receptor protein 1 | protein | 639 | 40% helix, 18% strand | P02786 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.85 | 0.96 | 57 | empty |
| 2 | 587 | 0.80 | 0.85 | 50 | empty |
| 3 | 871 | 0.79 | 0.82 | 91 | empty |
| 4 | 68 | 0.71 | 0.96 | 17 | empty |
| 5 | 152 | 0.55 | 0.81 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–D · 3051 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 625 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 622 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 glycan (N-glycosylation).
Compared structures
- 7ZQS · Cryo-EM Structure of Human Transferrin Receptor 1 bound to DNA Aptamer · the same entry in another collection · chain B against B, TM-score 1.00
- P02786 · AlphaFold monomer V2.0 prediction for transferrin receptor protein 1 (P02786) · a predicted model of the same protein · chain B against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 7ZQS · PDBe 7ZQS · UniProt P02786
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