MolNFT v1 · #159281 · protein
Crystal structure of human transferrin receptor in complex with a cystine-dense peptide
6OKD · Transferrin receptor protein 1: “Crystal structure of human transferrin receptor in complex with a cystine-dense peptide”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.80). MolNFT v1 #159281 on GenesisL1: 3D…
- PDB
- 6OKD
- Type
- protein
- Length
- 1,321 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferrin receptor protein 1; Transferrin receptor binding cystine-dense peptide
- UniProt
- P02786
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transferrin receptor protein 1 | protein | 619 | 39% helix, 20% strand | P02786 |
| B | Transferrin receptor protein 1 | protein | 617 | 39% helix, 20% strand | P02786 |
| C | Transferrin receptor binding cystine-dense peptide | protein | 43 | 67% helix, 0% strand | — |
| D | Transferrin receptor binding cystine-dense peptide | protein | 42 | 71% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.80 | 0.85 | 60 | GOL |
| 2 | 824 | 0.79 | 0.82 | 72 | GOL |
| 3 | 1132 | 0.79 | 0.80 | 135 | empty |
| 4 | 530 | 0.71 | 0.80 | 51 | empty |
| 5 | 499 | 0.70 | 0.80 | 61 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 2155 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1021 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 964 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6OKD · Crystal Structure of human transferrin receptor in complex with a cystine-dense peptide · 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 B against A, TM-score 0.98
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 6OKD · PDBe 6OKD · UniProt P02786
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