MolNFT v1 · #84623 · protein
Prgi-sipd from salmonella typhimurium
3ZQB · Protein prgi, cell invasion protein sipd: “Prgi-sipd from salmonella typhimurium”. X-ray diffraction, 3 pockets (best druggability 0.78). MolNFT v1 #84623 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZQB
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein prgi, cell invasion protein sipd
- UniProt
- P41784, Q56026
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein prgi, cell invasion protein sipd | protein | 272 | 70% helix, 7% strand | P41784, Q56026 |
| B | Protein prgi, cell invasion protein sipd | protein | 262 | 69% helix, 9% strand | P41784, Q56026 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.78 | 0.80 | 85 | GOL |
| 2 | 74 | 0.33 | 0.75 | 16 | empty |
| 3 | 71 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1482 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3ZQB · PrgI-SipD from Salmonella typhimurium · 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 0.75
- P41784 · AlphaFold monomer V2.0 prediction for protein prgi (P41784) · a predicted model of the same protein · chain B against A, TM-score 0.25
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 P41784
- Every structure of UniProt Q56026
- Elsewhere: RCSB PDB 3ZQB · PDBe 3ZQB · UniProt P41784 · UniProt Q56026
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