MolNFT v1 · #21051 · protein
SPA15, a type III secretion chaperone from shigella flexneri
1RY9 · Surface presentation of antigens protein spak: “SPA15, a type III secretion chaperone from shigella flexneri”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.75). MolNFT v1 #21051 on GenesisL1: 3D structure…
- PDB
- 1RY9
- Type
- protein
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface presentation of antigens protein spak
- UniProt
- P35530
- Ligands
- CL
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Surface presentation of antigens protein spak | protein | 133 | 42% helix, 29% strand | P35530 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.75 | 0.97 | 16 | empty |
| 2 | 75 | 0.74 | 0.97 | 16 | empty |
| 3 | 359 | 0.69 | 0.82 | 54 | CL |
| 4 | 368 | 0.63 | 0.78 | 47 | CL |
| 5 | 68 | 0.43 | 0.80 | 12 | empty |
Interfaces
4 interfaces between chains.
- C–D · 915 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 912 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 258 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1RY9 · Spa15, a Type III Secretion Chaperone from Shigella flexneri · the same entry in another collection · chain A against A, TM-score 1.00
- P35530 · AlphaFold monomer V2.0 prediction for surface presentation of antigens protein spak… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P35530
- Elsewhere: RCSB PDB 1RY9 · PDBe 1RY9 · UniProt P35530
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