MolNFT v1 · #77599 · protein
Crystal structure of pro-TGF beta 1
3RJR · Transforming growth factor beta-1: “Crystal structure of pro-TGF beta 1”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.71). MolNFT v1 #77599 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3RJR
- Type
- protein
- Length
- 1,355 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming growth factor beta-1
- UniProt
- P07200
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transforming growth factor beta-1 | protein | 340 | 21% helix, 34% strand | P07200 |
| B | Transforming growth factor beta-1 | protein | 330 | 22% helix, 34% strand | P07200 |
| C | Transforming growth factor beta-1 | protein | 343 | 22% helix, 34% strand | P07200 |
| D | Transforming growth factor beta-1 | protein | 342 | 23% helix, 34% strand | P07200 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.71 | 0.84 | 40 | empty |
| 2 | 294 | 0.70 | 0.84 | 36 | empty |
| 3 | 296 | 0.70 | 0.84 | 38 | empty |
| 4 | 292 | 0.69 | 0.83 | 37 | empty |
| 5 | 144 | 0.66 | 0.88 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4851 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 4838 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 386 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 366 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- P07200 · AlphaFold monomer V2.0 prediction for transforming growth factor beta-1 proprotein… · a predicted model of the same protein · chain B against A, TM-score 0.68
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 P07200
- Elsewhere: RCSB PDB 3RJR · PDBe 3RJR · UniProt P07200
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