Research workbench
Crystal structure analysis of bmp-2 in complex with bmpr-ia variant B1
Analyse Crystal structure analysis of bmp-2 in complex with bmpr-ia variant B1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QJ9
- Type
- protein
- Length
- 386 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone morphogenetic protein 2; Bone morphogenetic protein receptor type ia
- UniProt
- P12643, P36894
- Pockets
- 7 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Bone morphogenetic protein 2 | protein | 103 | 17% helix, 46% strand | P12643 |
| A | Bone morphogenetic protein 2 | protein | 104 | 18% helix, 43% strand | P12643 |
| D | Bone morphogenetic protein receptor type ia | protein | 93 | 10% helix, 35% strand | P36894 |
| C | Bone morphogenetic protein receptor type ia | protein | 86 | 9% helix, 37% strand | P36894 |
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.48 | 0.77 | 24 | empty |
| 2 | 160 | 0.45 | 0.75 | 30 | empty |
| 3 | 154 | 0.43 | 0.75 | 21 | empty |
| 4 | 72 | 0.35 | 0.76 | 19 | empty |
| 5 | 80 | 0.34 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–A · 1224 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 911 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 907 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 408 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 2QJ9 · Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B1 · the same entry in another collection · chain C against C, TM-score 1.00
- P12643 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein 2 (P12643) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P36894 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein receptor type-1A (P36894) · a predicted model of the same protein · chain C 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 P12643
- Every structure of UniProt P36894
- Elsewhere: RCSB PDB 2QJ9 · PDBe 2QJ9 · UniProt P12643 · UniProt P36894
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