Research workbench
Ternary structure of GDF11 bound to actriib-ecd and ALK5-ecd
Analyse Ternary structure of GDF11 bound to actriib-ecd and ALK5-ecd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MAC
- Type
- protein
- Length
- 283 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GROWTH/DIFFERENTIATION factor 11; Activin receptor type-2B; TGF-beta receptor type-1
- EC
- 2.7.11.30
- UniProt
- O95390, P38445, P36897
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GROWTH/DIFFERENTIATION factor 11 | protein | 108 | 11% helix, 45% strand | O95390 |
| C | Activin receptor type-2B (EC 2.7.11.30) | protein | 95 | 7% helix, 45% strand | P38445 |
| K | TGF-beta receptor type-1 (EC 2.7.11.30) | protein | 80 | 4% helix, 43% strand | P36897 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.60 | 0.86 | 19 | empty |
| 2 | 88 | 0.46 | 0.81 | 23 | empty |
| 3 | 75 | 0.37 | 0.77 | 21 | empty |
| 4 | 99 | 0.33 | 0.72 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 775 Ų buried · 5 hydrogen bonds · protein-protein
- A–K · 534 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6MAC · Ternary structure of GDF11 bound to ActRIIB-ECD and Alk5-ECD · the same entry in another collection · chain A against A, TM-score 1.00
- P38445 · AlphaFold monomer V2.0 prediction for activin receptor type-2B (P38445) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P36897 · AlphaFold monomer V2.0 prediction for TGF-beta receptor type-1 (P36897) · a predicted model of the same protein · chain K against A, TM-score 0.94
- O95390 · AlphaFold monomer V2.0 prediction for GROWTH/DIFFERENTIATION factor 11 (O95390) · a predicted model of the same protein · chain A against A, TM-score 0.77
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 O95390
- Every structure of UniProt P38445
- Every structure of UniProt P36897
- Elsewhere: RCSB PDB 6MAC · PDBe 6MAC · UniProt O95390 · UniProt P38445 · UniProt P36897
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