Research workbench
Crystal structure of computationally designed protein 2DS25.1 in complex with the human transferrin receptor ectodomain
Analyse Crystal structure of computationally designed protein 2DS25.1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WRX
- Type
- protein
- Length
- 1,455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferrin receptor protein 1; Computationally designed protein 2DS25.1
- UniProt
- P02786
- Ligands
- NAG, BMA, MAN, CA
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transferrin receptor protein 1 | protein | 639 | 37% helix, 19% strand | P02786 |
| B | Transferrin receptor protein 1 | protein | 640 | 37% helix, 19% strand | P02786 |
| C, D | Computationally designed protein 2DS25.1 | protein | 88 | 60% helix, 16% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.84 | 0.95 | 50 | empty |
| 2 | 983 | 0.82 | 0.84 | 104 | empty |
| 3 | 901 | 0.81 | 0.83 | 75 | empty |
| 4 | 343 | 0.75 | 0.86 | 53 | empty |
| 5 | 50 | 0.62 | 0.94 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3033 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 978 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 910 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6WRX · Crystal structure of computationally designed protein 2DS25.1 in complex with the human… · the same entry in another collection · chain A against A, 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
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 6WRX · PDBe 6WRX · UniProt P02786
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