Research workbench
Crystal structure of the yersinia enterocolitica type III secretion chaperone sycd in complex with a peptide of the translocator yopd
Analyse Crystal structure of the yersinia enterocolitica type III secretion chaperone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AM9
- Type
- protein
- Length
- 140 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone sycd; Yop effector yopd
- UniProt
- O87496, Q9R2G2
- Ligands
- ACE, SO4
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone sycd | protein | 131 | 77% helix, 0% strand | O87496 |
| B | Yop effector yopd | protein | 9 | 0% helix, 0% strand | Q9R2G2 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B
- SO4 · Sulfate ion · ion · chains A
- BU3 · (R,R)-2,3-butanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.36 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 612 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4AM9 · Crystal structure of the yersinia enterocolitica type III secretion chaperone sycd in… · 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 O87496
- Every structure of UniProt Q9R2G2
- Elsewhere: RCSB PDB 4AM9 · PDBe 4AM9 · UniProt O87496 · UniProt Q9R2G2
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