MolNFT v1 · #182476 · protein
Structure of GDF11 bound to fused actriib-ecd and ALK4-ecd with anti- actriib Fab fragment
7MRZ · GROWTH/DIFFERENTIATION factor 11: “Structure of GDF11 bound to fused actriib-ecd and ALK4-ecd with anti- actriib Fab fragment”. X-ray diffraction, 2 ligands (NAG, SO4), 6 pockets (best druggability 0.63). MolNFT v1 #182476 on…
- PDB
- 7MRZ
- Type
- protein
- Length
- 722 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GROWTH/DIFFERENTIATION factor 11; Activin receptor type-2B,ACTIVIN receptor type-1B; Fab…
- EC
- 2.7.11.30
- UniProt
- O95390, Q13705, P36896
- Ligands
- NAG, SO4
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GROWTH/DIFFERENTIATION factor 11 | protein | 108 | 12% helix, 45% strand | O95390 |
| C | Activin receptor type-2B,ACTIVIN receptor type-1B (EC 2.7.11.30) | protein | 171 | 4% helix, 30% strand | Q13705, P36896 |
| X | Fab heavy chain | protein | 222 | 4% helix, 46% strand | — |
| Y | Fab light chain | protein | 221 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C, X
- SO4 · Sulfate ion · ion · chains C, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.63 | 0.74 | 67 | empty |
| 2 | 219 | 0.55 | 0.78 | 30 | empty |
| 3 | 95 | 0.55 | 0.85 | 18 | empty |
| 4 | 269 | 0.54 | 0.76 | 39 | SO4 |
| 5 | 134 | 0.47 | 0.78 | 31 | empty |
Interfaces
4 interfaces between chains.
- X–Y · 1970 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1244 Ų buried · 6 hydrogen bonds · protein-protein
- C–X · 719 Ų buried · 14 hydrogen bonds · protein-protein
- C–Y · 203 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 19 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MRZ · Structure of GDF11 bound to fused ActRIIB-ECD and Alk4-ECD with Anti-ActRIIB Fab fragment · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- Q13705 · AlphaFold monomer V2.0 prediction for activin receptor type-2B (Q13705) · a predicted model of the same protein · chain C against A, TM-score 0.59
- P36896 · AlphaFold monomer V2.0 prediction for activin receptor type-1B (P36896) · a predicted model of the same protein · chain C against A, TM-score 0.42
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 Q13705
- Every structure of UniProt P36896
- Elsewhere: RCSB PDB 7MRZ · PDBe 7MRZ · UniProt O95390 · UniProt Q13705 · UniProt P36896
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