Research workbench
Crystal structure of computationally designed protein 3DS18 in complex with the human transferrin receptor ectodomain
Analyse Crystal structure of computationally designed protein 3DS18 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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