Research workbench
Crystal structure of the salmonella type III secretion system tip protein sipd
Analyse Crystal structure of the salmonella type III secretion system tip protein sipd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NZZ
- Type
- protein
- Length
- 563 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
- 4 · best druggability 0.64
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 | 286 | 69% helix, 8% strand | Q56026 |
| B | Cell invasion protein sipd | protein | 277 | 66% 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.64 | 0.76 | 50 | empty |
| 2 | 245 | 0.60 | 0.80 | 35 | empty |
| 3 | 187 | 0.47 | 0.76 | 29 | empty |
| 4 | 148 | 0.41 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 577 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3NZZ · Crystal Structure of the Salmonella Type III Secretion System Tip Protein SipD · 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 3NZZ · PDBe 3NZZ · UniProt Q56026
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