Research workbench
Crystal structure of the C-terminal domain of the shigella type III effector ipah
Analyse Crystal structure of the C-terminal domain of the shigella type III effector… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CKD
- Type
- protein
- Length
- 778 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Invasion plasmid antigen, secreted by the mxi-spa secretion machinery
- EC
- 6.3.2.19
- UniProt
- Q8VSA1
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Invasion plasmid antigen, secreted by the mxi-spa secretion machinery (EC 6.3.2.19) | protein | 262 | 73% helix, 0% strand | Q8VSA1 |
| B | Invasion plasmid antigen, secreted by the mxi-spa secretion machinery (EC 6.3.2.19) | protein | 244 | 76% helix, 0% strand | Q8VSA1 |
| C | Invasion plasmid antigen, secreted by the mxi-spa secretion machinery (EC 6.3.2.19) | protein | 272 | 78% helix, 0% strand | Q8VSA1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- GOL · Glycerol · additive · 3 copies · chains C
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.55 | 0.79 | 26 | empty |
| 2 | 156 | 0.48 | 0.78 | 23 | empty |
| 3 | 147 | 0.45 | 0.76 | 24 | empty |
| 4 | 176 | 0.45 | 0.75 | 22 | empty |
| 5 | 141 | 0.44 | 0.77 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1122 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3CKD · Crystal structure of the C-terminal domain of the Shigella type III effector IpaH · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8VSA1
- Elsewhere: RCSB PDB 3CKD · PDBe 3CKD · UniProt Q8VSA1
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