Research workbench
Periplasmic zinc binding protein troa from treponema pallidum
Analyse Periplasmic zinc binding protein troa from treponema pallidum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TOA
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (periplasmic binding protein troa)
- UniProt
- P96116
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (periplasmic binding protein troa) | protein | 277 | 51% helix, 15% strand | P96116 |
Ligands and binding sites
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 | 138 | 0.71 | 0.91 | 34 | empty |
| 2 | 68 | 0.37 | 0.78 | 24 | empty |
| 3 | 50 | 0.31 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1363 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1TOA · Periplasmic zinc binding protein troa from treponema pallidum · the same entry in another collection · chain A against A, TM-score 1.00
- P96116 · AlphaFold monomer V2.0 prediction for periplasmic zinc-binding protein troa (P96116) · a predicted model of the same protein · chain A 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 P96116
- Elsewhere: RCSB PDB 1TOA · PDBe 1TOA · UniProt P96116
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