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Crystal structure of the kinase domain of bone morphogenetic protein receptor type II (BMPR2) at 2.35 a resolution
Analyse Crystal structure of the kinase domain of bone morphogenetic protein receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G2F
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone morphogenetic protein receptor type-2
- EC
- 2.7.11.30
- UniProt
- Q13873
- Ligands
- ADP, MG, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bone morphogenetic protein receptor type-2 (EC 2.7.11.30) | protein | 305 | 40% helix, 19% strand | Q13873 |
| B | Bone morphogenetic protein receptor type-2 (EC 2.7.11.30) | protein | 303 | 40% helix, 17% strand | Q13873 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
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 | 300 | 0.69 | 0.83 | 35 | ADP, MG, SO4 |
| 2 | 309 | 0.68 | 0.82 | 39 | ADP, MG, SO4 |
| 3 | 53 | 0.67 | 0.96 | 16 | empty |
| 4 | 67 | 0.57 | 0.88 | 22 | empty |
| 5 | 59 | 0.41 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 3G2F · Crystal structure of the kinase domain of bone morphogenetic protein receptor type II… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13873 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein receptor type-2 (Q13873) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q13873
- Elsewhere: RCSB PDB 3G2F · PDBe 3G2F · UniProt Q13873
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