MolNFT v1 · #21185 · protein
Crystal structure of avrpphf ORF1, the chaperone for the type III effector avrpphf ORF2 from P. syringae
1S28: “Crystal structure of avrpphf ORF1, the chaperone for the type III effector avrpphf ORF2 from P. syringae”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.69). MolNFT v1 #21185 on GenesisL1: 3D structure, binding…
- 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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