MolNFT v1 · #77272 · protein
Cocrystal structure of proteolytically truncated form of ipad from shigella flexneri bound to deoxycholate
3R9V · Invasin ipad: “Cocrystal structure of proteolytically truncated form of ipad from shigella flexneri bound to deoxycholate”. X-ray diffraction, 1 ligand (DXC), 3 pockets (best druggability 0.46). MolNFT v1 #77272 on GenesisL1: 3D…
- 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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