Research workbench
Ternary complex of human bone morphogenetic protein 9 (BMP9) growth factor domain, its prodomain and extracellular domain of activin receptor-like kinase 1 (ALK1).
Analyse Ternary complex of human bone morphogenetic protein 9 (BMP9) growth factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SF2
- Type
- protein
- Length
- 591 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase receptor R3; GROWTH/DIFFERENTIATION factor 2
- EC
- 2.7.11.30
- UniProt
- P37023, Q9UK05
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 75 | 5% helix, 39% strand | P37023 |
| B, E | GROWTH/DIFFERENTIATION factor 2 | protein | 105 | 18% helix, 46% strand | Q9UK05 |
| C | GROWTH/DIFFERENTIATION factor 2 | protein | 73 | 23% helix, 23% strand | Q9UK05 |
| D | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 77 | 5% helix, 38% strand | P37023 |
| F | GROWTH/DIFFERENTIATION factor 2 | protein | 156 | 12% helix, 42% strand | Q9UK05 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.71 | 0.82 | 48 | empty |
| 2 | 189 | 0.68 | 0.87 | 30 | empty |
| 3 | 65 | 0.47 | 0.83 | 17 | empty |
| 4 | 174 | 0.44 | 0.74 | 29 | empty |
| 5 | 115 | 0.43 | 0.77 | 21 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1282 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 727 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 635 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 589 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 531 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6SF2 · Ternary complex of human bone morphogenetic protein 9 (BMP9) growth factor domain, its… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UK05 · AlphaFold monomer V2.0 prediction for GROWTH/DIFFERENTIATION factor 2 (Q9UK05) · a predicted model of the same protein · chain E against A, TM-score 0.97
- P37023 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase receptor R3 (P37023) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P37023
- Every structure of UniProt Q9UK05
- Elsewhere: RCSB PDB 6SF2 · PDBe 6SF2 · UniProt P37023 · UniProt Q9UK05
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