Research workbench
Ternary complex of bmp-2 bound to bmpr-ia-ecd and actrii-ecd
Analyse Ternary complex of bmp-2 bound to bmpr-ia-ecd and actrii-ecd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GOO
- Type
- protein
- Length
- 565 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone morphogenetic protein 2; Bone morphogenetic protein receptor type ia; Activin…
- EC
- 2.7.11.30
- UniProt
- P12643, P36894, P27038
- Ligands
- NDG
- Pockets
- 11 · best druggability 0.57
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bone morphogenetic protein 2 | protein | 103 | 18% helix, 46% strand | P12643 |
| B | Bone morphogenetic protein receptor type ia (EC 2.7.11.30) | protein | 85 | 7% helix, 38% strand | P36894 |
| C | Activin receptor type 2A (EC 2.7.11.30) | protein | 92 | 8% helix, 47% strand | P27038 |
| D | Bone morphogenetic protein 2 | protein | 104 | 18% helix, 45% strand | P12643 |
| E | Bone morphogenetic protein receptor type ia (EC 2.7.11.30) | protein | 88 | 11% helix, 38% strand | P36894 |
| F | Activin receptor type 2A (EC 2.7.11.30) | protein | 93 | 8% helix, 46% strand | P27038 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.57 | 0.79 | 44 | empty |
| 2 | 169 | 0.56 | 0.81 | 29 | empty |
| 3 | 119 | 0.49 | 0.80 | 22 | empty |
| 4 | 145 | 0.48 | 0.78 | 21 | empty |
| 5 | 142 | 0.46 | 0.77 | 31 | empty |
Interfaces
5 interfaces between chains.
- D–E · 965 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 889 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 744 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 738 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 421 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 2GOO · Ternary Complex of BMP-2 bound to BMPR-Ia-ECD and ActRII-ECD · the same entry in another collection · chain F against F, TM-score 1.00
- P27038 · AlphaFold monomer V2.0 prediction for activin receptor type-2A (P27038) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P36894 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein receptor type-1A (P36894) · a predicted model of the same protein · chain B against A, TM-score 0.95
- 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 0.95
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
- Every structure of UniProt P27038
- Elsewhere: RCSB PDB 2GOO · PDBe 2GOO · UniProt P12643 · UniProt P36894 · UniProt P27038
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