Research workbench
Crystal structure of the salmonella type III secretion system tip protein sipd-C244S
Analyse Crystal structure of the salmonella type III secretion system tip protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O00
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell invasion protein sipd
- UniProt
- Q56026
- Ligands
- NI
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell invasion protein sipd | protein | 285 | 68% helix, 8% strand | Q56026 |
| B | Cell invasion protein sipd | protein | 266 | 67% helix, 9% strand | Q56026 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.66 | 0.76 | 51 | empty |
| 2 | 258 | 0.60 | 0.79 | 36 | empty |
| 3 | 151 | 0.42 | 0.74 | 24 | empty |
| 4 | 110 | 0.40 | 0.76 | 20 | empty |
| 5 | 77 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 606 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3O00 · Crystal Structure of the Salmonella Type III Secretion System Tip Protein SipD-C244S · the same entry in another collection · chain A against A, TM-score 1.00
- Q56026 · AlphaFold monomer V2.0 prediction for cell invasion protein sipd (Q56026) · a predicted model of the same protein · chain B 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 Q56026
- Elsewhere: RCSB PDB 3O00 · PDBe 3O00 · UniProt Q56026
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