Research workbench
High resolution structure of bone morphogenetic protein receptor type II (bmprii) extracellular domain in complex with BMP10
Analyse High resolution structure of bone morphogenetic protein receptor type II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PPA
- Type
- protein
- Length
- 412 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone morphogenetic protein 10; Bone morphogenetic protein receptor type-2
- EC
- 2.7.11.30
- UniProt
- O95393, Q13873
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bone morphogenetic protein 10 | protein | 104 | 18% helix, 48% strand | O95393 |
| B | Bone morphogenetic protein 10 | protein | 105 | 18% helix, 48% strand | O95393 |
| C | Bone morphogenetic protein receptor type-2 (EC 2.7.11.30) | protein | 105 | 10% helix, 36% strand | Q13873 |
| D | Bone morphogenetic protein receptor type-2 (EC 2.7.11.30) | protein | 98 | 10% helix, 37% strand | Q13873 |
Ligands and binding sites
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.55 | 0.89 | 23 | empty |
| 2 | 106 | 0.53 | 0.83 | 23 | empty |
| 3 | 117 | 0.39 | 0.75 | 29 | empty |
| 4 | 100 | 0.38 | 0.75 | 22 | empty |
| 5 | 68 | 0.31 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1487 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 948 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 788 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 7PPA · High resolution structure of bone morphogenetic protein receptor type II (BMPRII)… · the same entry in another collection · chain D against D, TM-score 1.00
- O95393 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein 10 (O95393) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q13873 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein receptor type-2 (Q13873) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 O95393
- Every structure of UniProt Q13873
- Elsewhere: RCSB PDB 7PPA · PDBe 7PPA · UniProt O95393 · UniProt Q13873
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