MolNFT v1 · #71425 · protein
Crystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor type-1B (BMPR1B) in complex with FKBP12 and ldn- 193189
3MDY: “Crystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor type-1B (BMPR1B) in…”. X-ray diffraction, 1 ligand (LDN), 15 pockets (best druggability 0.76). MolNFT v1 #71425 on GenesisL1: 3D structure…
- PDB
- 3MDY
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone morphogenetic protein receptor type-1B; Peptidyl-prolyl cis-trans isomerase FKBP1A
- EC
- 2.7.11.30, 5.2.1.8
- UniProt
- O00238, P62942
- Ligands
- LDN
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bone morphogenetic protein receptor type-1B (EC 2.7.11.30) | protein | 320 | 42% helix, 18% strand | O00238 |
| C | Bone morphogenetic protein receptor type-1B (EC 2.7.11.30) | protein | 320 | 42% helix, 18% strand | O00238 |
| B, D | Peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 109 | 10% helix, 39% strand | P62942 |
Ligands and binding sites
- LDN · 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.76 | 0.81 | 64 | empty |
| 2 | 205 | 0.67 | 0.85 | 29 | LDN |
| 3 | 215 | 0.67 | 0.85 | 31 | LDN |
| 4 | 157 | 0.56 | 0.81 | 21 | empty |
| 5 | 171 | 0.54 | 0.80 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 925 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 898 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 368 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 361 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 120 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3MDY · Crystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor… · the same entry in another collection · chain D against D, TM-score 1.00
- O00238 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein receptor type-1B (O00238) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P62942 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP1A (P62942) · a predicted model of the same protein · chain B 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 O00238
- Every structure of UniProt P62942
- Elsewhere: RCSB PDB 3MDY · PDBe 3MDY · UniProt O00238 · UniProt P62942
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.