Research workbench
Crystal structure of ipgc in complex with a follow-up compound based on J20
Analyse Crystal structure of ipgc in complex with a follow-up compound based on J20 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OWV
- 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
- 2IY, CL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 78% 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 | 140 | 78% helix, 0% strand | P0A2U4 |
Ligands and binding sites
- 2IY · 3-(4-chlorophenyl)-5-methylsulfanyl-1~{H}-pyrazole-4-carbonitrile · ligand · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.63 | 0.88 | 19 | 2IY |
| 2 | 189 | 0.54 | 0.79 | 26 | empty |
| 3 | 135 | 0.46 | 0.77 | 20 | empty |
| 4 | 62 | 0.31 | 0.75 | 18 | DMS |
Interfaces
1 interface between chains.
- A–B · 941 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7OWV · Crystal structure of IpgC in complex with a follow-up compound based on J20 · 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 0.92
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 7OWV · PDBe 7OWV · UniProt P0A2U4
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