Research workbench
Crystal structure of human prolactin receptor complexed with Fab fragment
Analyse Crystal structure of human prolactin receptor complexed with Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I18
- Type
- protein
- Length
- 1,270 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody light chain; Antibody heavy chain; Prolactin receptor
- UniProt
- P16471
- Ligands
- CA
- Pockets
- 15 · best druggability 0.61
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody light chain | protein | 216 | 6% helix, 51% strand | — |
| H | Antibody heavy chain | protein | 227 | 5% helix, 51% strand | — |
| B | Antibody light chain | protein | 215 | 6% helix, 51% strand | — |
| A | Antibody heavy chain | protein | 219 | 5% helix, 52% strand | — |
| R | Prolactin receptor | protein | 205 | 4% helix, 43% strand | P16471 |
| C | Prolactin receptor | protein | 188 | 4% helix, 43% strand | P16471 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains H, A, B
- GOL · Glycerol · additive · 4 copies · chains L, H, C, A, R
- ACT · Acetate ion · additive · chains B, A, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.61 | 0.74 | 60 | empty |
| 2 | 498 | 0.60 | 0.74 | 62 | empty |
| 3 | 480 | 0.57 | 0.73 | 52 | empty |
| 4 | 256 | 0.57 | 0.78 | 31 | GOL |
| 5 | 74 | 0.56 | 0.88 | 21 | empty |
Interfaces
7 interfaces between chains.
- L–H · 2011 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 1820 Ų buried · 11 hydrogen bonds · protein-protein
- A–R · 823 Ų buried · 10 hydrogen bonds · protein-protein
- H–C · 805 Ų buried · 11 hydrogen bonds · protein-protein
- H–A · 593 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4I18 · Crystal structure of human prolactin receptor complexed with Fab fragment · the same entry in another collection · chain C against C, TM-score 1.00
- P16471 · AlphaFold monomer V2.0 prediction for prolactin receptor (P16471) · a predicted model of the same protein · chain R against A, TM-score 0.86
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 P16471
- Elsewhere: RCSB PDB 4I18 · PDBe 4I18 · UniProt P16471
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