MolNFT v1 · #18078 · protein
Crystal structure of human platelet-derived growth factor bb
1PDG: “Crystal structure of human platelet-derived growth factor bb”. X-ray diffraction, 2 pockets (best druggability 0.31). MolNFT v1 #18078 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1PDG
- Type
- protein
- Length
- 256 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-derived growth factor bb
- UniProt
- P01127
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-derived growth factor bb | protein | 87 | 0% helix, 64% strand | P01127 |
| B | Platelet-derived growth factor bb | protein | 83 | 0% helix, 54% strand | P01127 |
| C | Platelet-derived growth factor bb | protein | 86 | 0% helix, 40% strand | P01127 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.31 | 0.75 | 18 | empty |
| 2 | 60 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1114 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 1PDG · Crystal structure of human platelet-derived growth factor bb · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.95
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
- Elsewhere: RCSB PDB 1PDG · PDBe 1PDG · UniProt P01127
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