MolNFT v1 · #38687 · protein
Crystal structure of a ternary ligand-receptor complex of bmp-2
2H62 · Bone morphogenetic protein 2: “Crystal structure of a ternary ligand-receptor complex of bmp-2”. X-ray diffraction, 6 pockets (best druggability 0.57). MolNFT v1 #38687 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2H62
- Type
- protein
- Length
- 384 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; ACVR2B protein
- EC
- 2.7.11.30
- UniProt
- P12643, P36894, Q3KQI1
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bone morphogenetic protein 2 | protein | 104 | 15% helix, 47% strand | P12643 |
| B | Bone morphogenetic protein 2 | protein | 103 | 17% helix, 48% strand | P12643 |
| C | Bone morphogenetic protein receptor type ia (EC 2.7.11.30) | protein | 84 | 12% helix, 39% strand | P36894 |
| D | ACVR2B protein | protein | 93 | 8% helix, 46% strand | Q3KQI1 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.57 | 0.82 | 31 | empty |
| 2 | 52 | 0.45 | 0.84 | 19 | empty |
| 3 | 121 | 0.44 | 0.77 | 29 | empty |
| 4 | 120 | 0.40 | 0.75 | 25 | empty |
| 5 | 99 | 0.37 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1238 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 927 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 809 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 2H62 · Crystal structure of a ternary ligand-receptor complex of BMP-2 · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.95
- 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 0.94
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
- Every structure of UniProt Q3KQI1
- Elsewhere: RCSB PDB 2H62 · PDBe 2H62 · UniProt P12643 · UniProt P36894 · UniProt Q3KQI1
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