MolNFT v1 · #168811 · protein
Crystal structure of computationally designed protein 3DS18 in complex with the human transferrin receptor ectodomain
6WRV · Transferrin receptor protein 1: “Crystal structure of computationally designed protein 3DS18 in complex with the human transferrin receptor…”. X-ray diffraction, 3 ligands (NAG, BMA, CA), 20 pockets (best druggability 0.85). MolNFT…
- PDB
- 6WRV
- Type
- protein
- Length
- 2,194 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferrin receptor protein 1; Computationally designed protein 3DS18
- UniProt
- P02786
- Ligands
- NAG, BMA, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transferrin receptor protein 1 | protein | 639 | 39% helix, 19% strand | P02786 |
| E | Transferrin receptor protein 1 | protein | 637 | 39% helix, 19% strand | P02786 |
| D, C, F | Computationally designed protein 3DS18 | protein | 93 | 61% helix, 15% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, F, E
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains B
- CA · Calcium ion · metal · 3 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.85 | 0.95 | 60 | empty |
| 2 | 991 | 0.81 | 0.82 | 93 | CA |
| 3 | 707 | 0.80 | 0.84 | 60 | empty |
| 4 | 821 | 0.79 | 0.82 | 67 | empty |
| 5 | 291 | 0.77 | 0.89 | 56 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3080 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 885 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 855 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 828 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 733 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6WRV · Crystal structure of computationally designed protein 3DS18 in complex with the human… · the same entry in another collection · chain F against F, TM-score 1.00
- P02786 · AlphaFold monomer V2.0 prediction for transferrin receptor protein 1 (P02786) · a predicted model of the same protein · chain E 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 6WRV · PDBe 6WRV · UniProt P02786
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