Research workbench
Xchem group deposition -- crystal structure of human ACVR1 in complex with FM010955A
Analyse Xchem group deposition -- crystal structure of human ACVR1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5S9K
- Type
- protein
- Length
- 573 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, YV4, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activin receptor type-1 (EC 2.7.11.30) | protein | 281 | 40% helix, 20% strand | Q04771 |
| B | Activin receptor type-1 (EC 2.7.11.30) | protein | 292 | 37% 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
- YV4 · (3S)-3-aminopyrrolidin-2-one · ligand · chains B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.67 | 0.82 | 33 | LU8, SO4 |
| 2 | 350 | 0.67 | 0.81 | 37 | LU8 |
| 3 | 546 | 0.67 | 0.77 | 60 | empty |
| 4 | 55 | 0.56 | 0.89 | 16 | empty |
| 5 | 92 | 0.41 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 398 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5S9K · XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010955a · 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 A 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 5S9K · PDBe 5S9K · UniProt Q04771
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