Research workbench
Crystal structure analysis of bmp-2 in complex with bmpr-ia variant B12
Analyse Crystal structure analysis of bmp-2 in complex with bmpr-ia variant B12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QJA
- 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 0.53
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bone morphogenetic protein 2 | protein | 104 | 18% helix, 45% strand | P12643 |
| C | Bone morphogenetic protein receptor type ia | protein | 85 | 11% helix, 39% strand | P36894 |
| D | Bone morphogenetic protein receptor type ia | protein | 93 | 10% helix, 34% strand | P36894 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.53 | 0.77 | 26 | empty |
| 2 | 159 | 0.43 | 0.75 | 23 | empty |
| 3 | 73 | 0.37 | 0.78 | 18 | empty |
| 4 | 71 | 0.37 | 0.77 | 17 | empty |
| 5 | 68 | 0.34 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1229 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 887 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 418 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 2QJA · Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B12 · the same entry in another collection · chain D against D, TM-score 1.00
- P12643 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein 2 (P12643) · a predicted model of the same protein · chain A 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 2QJA · PDBe 2QJA · UniProt P12643 · UniProt P36894
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