Research workbench
Crystal structure of avrpphf ORF1, the chaperone for the type III effector avrpphf ORF2 from P. syringae
Analyse Crystal structure of avrpphf ORF1, the chaperone for the 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
- 1S28
- Type
- protein
- Length
- 520 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1
- UniProt
- Q9K2L2
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ORF1 | protein | 130 | 39% helix, 26% strand | Q9K2L2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.69 | 0.77 | 80 | SO4 |
| 2 | 57 | 0.60 | 0.91 | 15 | empty |
| 3 | 51 | 0.37 | 0.80 | 12 | empty |
| 4 | 59 | 0.35 | 0.78 | 14 | empty |
| 5 | 55 | 0.29 | 0.74 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1895 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1872 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 385 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 1S28 · Crystal Structure of AvrPphF ORF1, the Chaperone for the Type III Effector AvrPphF ORF2… · 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 Q9K2L2
- Elsewhere: RCSB PDB 1S28 · PDBe 1S28 · UniProt Q9K2L2
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