MolNFT v1 · #133692 · protein
Xchem group deposition -- crystal structure of human ACVR1 in complex with FM010949A
5S84 · Activin receptor type-1: “Xchem group deposition -- crystal structure of human ACVR1 in complex with FM010949A”. X-ray diffraction, 3 ligands (LU8, XK1, SO4), 5 pockets (best druggability 0.69). MolNFT v1 #133692 on GenesisL1: 3D…
- PDB
- 5S84
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activin receptor type-1
- EC
- 2.7.11.30
- UniProt
- Q04771
- Ligands
- LU8, XK1, SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activin receptor type-1 (EC 2.7.11.30) | protein | 284 | 39% helix, 20% strand | Q04771 |
| B | Activin receptor type-1 (EC 2.7.11.30) | protein | 291 | 38% helix, 23% strand | Q04771 |
Ligands and binding sites
- LU8 · 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine · ligand · 4 copies · chains A, B
- XK1 · 1-[(4R)-1,3-oxazolidin-4-yl]methanamine · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.69 | 0.77 | 70 | empty |
| 2 | 347 | 0.68 | 0.81 | 43 | LU8 |
| 3 | 334 | 0.67 | 0.82 | 34 | LU8 |
| 4 | 70 | 0.50 | 0.84 | 18 | empty |
| 5 | 70 | 0.33 | 0.75 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 410 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5S84 · XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010949a · the same entry in another collection · chain A against A, TM-score 1.00
- Q04771 · AlphaFold monomer V2.0 prediction for activin receptor type-1 (Q04771) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q04771
- Elsewhere: RCSB PDB 5S84 · PDBe 5S84 · UniProt Q04771
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