Research workbench
Crystal structure of a shortened ipgc variant in complex with 2H- isoindol-1-amine
Analyse Crystal structure of a shortened ipgc variant in complex with 2H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AYW
- Type
- protein
- Length
- 281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein ipgc
- UniProt
- P0A2U4
- Ligands
- F05, MG, CL
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein ipgc | protein | 138 | 78% helix, 0% strand | P0A2U4 |
| B | Chaperone protein ipgc | protein | 143 | 74% helix, 0% strand | P0A2U4 |
Ligands and binding sites
- F05 · 1H-isoindol-3-amine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal
- CL · Chloride ion · ion · 5 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.64 | 0.91 | 17 | F05 |
| 2 | 352 | 0.63 | 0.78 | 52 | DMS |
| 3 | 58 | 0.34 | 0.77 | 13 | DMS |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7AYW · Crystal structure of a shortened IpgC variant in complex with 2H-isoindol-1-amine · the same entry in another collection · chain A against A, TM-score 1.00
- P0A2U4 · AlphaFold monomer V2.0 prediction for chaperone protein ipgc (P0A2U4) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P0A2U4
- Elsewhere: RCSB PDB 7AYW · PDBe 7AYW · UniProt P0A2U4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.