Research workbench
The structure of a platelet derived growth factor receptor complex
Analyse The structure of a platelet derived growth factor receptor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MJG
- Type
- protein
- Length
- 745 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-derived growth factor subunit B; Beta-type platelet-derived growth factor…
- EC
- 2.7.10.1
- UniProt
- P01127, P09619
- Ligands
- NAG, NDG
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-derived growth factor subunit B | protein | 97 | 3% helix, 67% strand | P01127 |
| B | Platelet-derived growth factor subunit B | protein | 101 | 4% helix, 63% strand | P01127 |
| X | Beta-type platelet-derived growth factor receptor (EC 2.7.10.1) | protein | 274 | 3% helix, 48% strand | P09619 |
| Y | Beta-type platelet-derived growth factor receptor (EC 2.7.10.1) | protein | 273 | 3% helix, 44% strand | P09619 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains X, Y
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.66 | 0.84 | 27 | empty |
| 2 | 154 | 0.60 | 0.84 | 19 | empty |
| 3 | 109 | 0.59 | 0.86 | 17 | empty |
| 4 | 162 | 0.52 | 0.79 | 28 | empty |
| 5 | 89 | 0.40 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1140 Ų buried · 14 hydrogen bonds · protein-protein
- B–X · 1046 Ų buried · 14 hydrogen bonds · protein-protein
- A–Y · 1016 Ų buried · 16 hydrogen bonds · protein-protein
- B–Y · 554 Ų buried · 12 hydrogen bonds · protein-protein
- A–X · 527 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 3MJG · The structure of a platelet derived growth factor receptor complex · the same entry in another collection · chain Y against Y, TM-score 1.00
- P01127 · AlphaFold monomer V2.0 prediction for platelet-derived growth factor subunit B (P01127) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P09619 · AlphaFold monomer V2.0 prediction for platelet-derived growth factor receptor beta… · a predicted model of the same protein · chain X against A, TM-score 0.94
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 P01127
- Every structure of UniProt P09619
- Elsewhere: RCSB PDB 3MJG · PDBe 3MJG · UniProt P01127 · UniProt P09619
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