MolNFT v1 · #115660 · protein
Crystal structure of SOPD2, a type III secreted virulence effector from salmonella enterica
5CQ9 · Secreted effector protein SOPD2: “Crystal structure of SOPD2, a type III secreted virulence effector from salmonella enterica”. X-ray diffraction, 7 pockets (best druggability 0.68). MolNFT v1 #115660 on GenesisL1: 3D structure…
- PDB
- 5CQ9
- Type
- protein
- Length
- 559 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted effector protein SOPD2; 11-mer peptide
- UniProt
- Q8ZQC8
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Secreted effector protein SOPD2 | protein | 269 | 50% helix, 13% strand | Q8ZQC8 |
| B | Secreted effector protein SOPD2 | protein | 270 | 49% helix, 13% strand | Q8ZQC8 |
| C | 11-mer peptide | protein | 9 | 78% helix, 0% strand | — |
| D | 11-mer peptide | protein | 11 | 82% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.68 | 0.79 | 65 | empty |
| 2 | 136 | 0.46 | 0.78 | 29 | empty |
| 3 | 83 | 0.41 | 0.78 | 18 | empty |
| 4 | 112 | 0.37 | 0.74 | 25 | empty |
| 5 | 115 | 0.36 | 0.73 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 290 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 276 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 121 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5CQ9 · Crystal structure of SopD2, a type III secreted virulence effector from Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZQC8 · AlphaFold monomer V2.0 prediction for secreted effector protein SOPD2 (Q8ZQC8) · 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 Q8ZQC8
- Elsewhere: RCSB PDB 5CQ9 · PDBe 5CQ9 · UniProt Q8ZQC8
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