MolNFT v1 · #168812 · protein
Crystal structure of computationally designed protein 2DS25.5 in complex with the human transferrin receptor ectodomain
6WRW · Transferrin receptor protein 1: “Crystal structure of computationally designed protein 2DS25.5 in complex with the human transferrin receptor…”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 18 pockets (best druggability 0.84).…
- PDB
- 6WRW
- 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 2DS25.5
- UniProt
- P02786
- Ligands
- NAG, BMA, MAN, CA
- Pockets
- 18 · 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 2DS25.5 | protein | 88 | 60% helix, 16% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 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
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.84 | 0.96 | 47 | empty |
| 2 | 881 | 0.81 | 0.83 | 71 | empty |
| 3 | 1015 | 0.81 | 0.82 | 91 | empty |
| 4 | 145 | 0.76 | 0.94 | 31 | empty |
| 5 | 380 | 0.61 | 0.77 | 60 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3175 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 954 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 948 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6WRW · Crystal structure of computationally designed protein 2DS25.5 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 6WRW · PDBe 6WRW · UniProt P02786
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