Research workbench
Human L-TGF-BETA1 in complex with the anchor protein LRRC33
Analyse Human L-TGF-BETA1 in complex with the anchor protein LRRC33 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Y1R
- Type
- protein
- Length
- 1,041 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming growth factor beta-1 proprotein; Transforming growth factor beta activator…
- UniProt
- P01137, Q86YC3
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 13% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transforming growth factor beta-1 proprotein | protein | 305 | 19% helix, 22% strand | P01137 |
| B | Transforming growth factor beta-1 proprotein | protein | 308 | 21% helix, 23% strand | P01137 |
| E | Transforming growth factor beta activator LRRC33 | protein | 428 | 4% helix, 15% strand | Q86YC3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, E
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.84 | 0.87 | 96 | empty |
| 2 | 457 | 0.83 | 0.90 | 53 | empty |
| 3 | 1051 | 0.78 | 0.79 | 131 | empty |
| 4 | 182 | 0.76 | 0.91 | 50 | empty |
| 5 | 633 | 0.72 | 0.79 | 69 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3605 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 801 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 500 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7Y1R · Human L-TGF-beta1 in complex with the anchor protein LRRC33 · the same entry in another collection · chain A against A, TM-score 1.00
- Q86YC3 · AlphaFold monomer V2.0 prediction for transforming growth factor beta activator LRRC33… · a predicted model of the same protein · chain E against A, TM-score 0.93
- P01137 · 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 0.66
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 P01137
- Every structure of UniProt Q86YC3
- Elsewhere: RCSB PDB 7Y1R · PDBe 7Y1R · UniProt P01137 · UniProt Q86YC3
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