Research workbench
Vibrio vulnificus wzb in complex with benzylphosphonate
Analyse Vibrio vulnificus wzb in complex with benzylphosphonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DHF
- Type
- protein
- Length
- 590 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine-phosphatase
- EC
- 3.1.3.48
- UniProt
- E5F0S0
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein-tyrosine-phosphatase (EC 3.1.3.48) | protein | 146 | 42% helix, 14% strand | E5F0S0 |
| C, D | Protein-tyrosine-phosphatase (EC 3.1.3.48) | protein | 149 | 39% helix, 13% strand | E5F0S0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.79 | 0.81 | 84 | empty |
| 2 | 102 | 0.61 | 0.87 | 17 | empty |
| 3 | 191 | 0.60 | 0.81 | 23 | empty |
| 4 | 223 | 0.57 | 0.79 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–C · 645 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 603 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 367 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 355 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7DHF · Vibrio vulnificus Wzb in complex with benzylphosphonate · the same entry in another collection · 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 E5F0S0
- Elsewhere: RCSB PDB 7DHF · PDBe 7DHF · UniProt E5F0S0
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