Research workbench
Crystal structure of ipgc in complex with a follow-up compound based on J2
Analyse Crystal structure of ipgc in complex with a follow-up compound based on J2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P42
- Type
- protein
- Length
- 278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein ipgc
- UniProt
- P0A2U4
- Ligands
- 5I8, MG, CL
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein ipgc | protein | 136 | 75% helix, 0% strand | P0A2U4 |
| B | Chaperone protein ipgc | protein | 142 | 75% helix, 0% strand | P0A2U4 |
Ligands and binding sites
- 5I8 · 2-(4,6-dimethylpyrimidin-2-yl)-3H-isoindol-1-imine · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.58 | 0.87 | 22 | DMS |
| 2 | 122 | 0.49 | 0.79 | 18 | empty |
| 3 | 125 | 0.48 | 0.79 | 21 | empty |
| 4 | 139 | 0.44 | 0.76 | 26 | empty |
| 5 | 78 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7P42 · Crystal structure of IpgC in complex with a follow-up compound based on J2 · 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 0.93
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 7P42 · PDBe 7P42 · UniProt P0A2U4
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