Research workbench
Cocrystal structure of proteolytically truncated form of ipad from shigella flexneri bound to deoxycholate
Analyse Cocrystal structure of proteolytically truncated form of ipad from shigella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R9V
- Type
- protein
- Length
- 361 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Invasin ipad
- UniProt
- P18013
- Ligands
- DXC
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Invasin ipad | protein | 198 | 66% helix, 13% strand | P18013 |
| B | Invasin ipad | protein | 163 | 69% helix, 9% strand | P18013 |
Ligands and binding sites
- DXC · (3alpha,5beta,12alpha)-3,12-dihydroxycholan-24-oic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.46 | 0.75 | 15 | DXC |
| 2 | 121 | 0.43 | 0.76 | 16 | empty |
| 3 | 60 | 0.34 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1194 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3R9V · Cocrystal Structure of Proteolytically Truncated Form of IpaD from Shigella flexneri… · the same entry in another collection · chain A against A, TM-score 1.00
- P18013 · AlphaFold monomer V2.0 prediction for invasin ipad (P18013) · 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 P18013
- Elsewhere: RCSB PDB 3R9V · PDBe 3R9V · UniProt P18013
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