MolNFT v1 · #103981 · protein
Crystal structure of tolb protein from yersinia pestis CO92
4PWZ · Protein tolb: “Crystal structure of tolb protein from yersinia pestis CO92”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.82). MolNFT v1 #103981 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PWZ
- Type
- protein
- Length
- 811 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein tolb
- UniProt
- Q8ZGZ1
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein tolb | protein | 405 | 10% helix, 45% strand | Q8ZGZ1 |
| B | Protein tolb | protein | 406 | 10% helix, 44% strand | Q8ZGZ1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.82 | 0.83 | 105 | GOL, MES, SO4 |
| 2 | 569 | 0.79 | 0.85 | 52 | empty |
| 3 | 538 | 0.78 | 0.85 | 55 | empty |
| 4 | 396 | 0.61 | 0.77 | 33 | empty |
| 5 | 182 | 0.61 | 0.83 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1146 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
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 Q8ZGZ1
- Elsewhere: RCSB PDB 4PWZ · PDBe 4PWZ · UniProt Q8ZGZ1
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