Research workbench
Structure of garp (LRRC32) in complex with latent TGF-BETA1 and mhg-8 Fab
Analyse Structure of garp (LRRC32) in complex with latent TGF-BETA1 and mhg-8 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GFF
- Type
- protein
- Length
- 2,953 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming growth factor beta-1; Leucine-rich repeat-containing protein 32; Mhg-8 Fab…
- UniProt
- P01137, Q14392
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 13 distinct chains · 13% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transforming growth factor beta-1 | protein | 168 | 29% helix, 30% strand | P01137 |
| B, F | Transforming growth factor beta-1 | protein | 112 | 12% helix, 44% strand | P01137 |
| C | Transforming growth factor beta-1 | protein | 209 | 28% helix, 30% strand | P01137 |
| D | Transforming growth factor beta-1 | protein | 111 | 13% helix, 41% strand | P01137 |
| E | Transforming growth factor beta-1 | protein | 222 | 25% helix, 31% strand | P01137 |
| G | Transforming growth factor beta-1 | protein | 218 | 29% helix, 28% strand | P01137 |
| H | Transforming growth factor beta-1 | protein | 109 | 9% helix, 43% strand | P01137 |
| I | Leucine-rich repeat-containing protein 32 | protein | 551 | 7% helix, 19% strand | Q14392 |
| J | Leucine-rich repeat-containing protein 32 | protein | 493 | 7% helix, 20% strand | Q14392 |
| K | Mhg-8 Fab light chain | protein | 212 | 5% helix, 47% strand | — |
| L | Mhg-8 Fab heavy chain | protein | 214 | 4% helix, 50% strand | — |
| M | Mhg-8 Fab light chain | protein | 104 | 3% helix, 40% strand | — |
| N | Mhg-8 Fab heavy chain | protein | 118 | 5% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains I, J
- BMA · beta-D-mannopyranose · sugar · 6 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.81 | 0.83 | 84 | empty |
| 2 | 1069 | 0.81 | 0.82 | 115 | empty |
| 3 | 747 | 0.79 | 0.83 | 69 | empty |
| 4 | 963 | 0.78 | 0.80 | 84 | empty |
| 5 | 275 | 0.71 | 0.85 | 49 | empty |
Interfaces
39 interfaces between chains.
- B–C · 1788 Ų buried · 19 hydrogen bonds · protein-protein
- E–H · 1754 Ų buried · 20 hydrogen bonds · protein-protein
- K–L · 1753 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1722 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1555 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6GFF · Structure of GARP (LRRC32) in complex with latent TGF-beta1 and MHG-8 Fab · the same entry in another collection · chain N against N, TM-score 1.00
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 Q14392
- Elsewhere: RCSB PDB 6GFF · PDBe 6GFF · UniProt P01137 · UniProt Q14392
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