Research workbench
Crystal structure of the yersinia pestis phosphatase yoph in complex with a phosphotyrosyl mimetic-containing hexapeptide
Analyse Crystal structure of the yersinia pestis phosphatase yoph in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QZ0
- Type
- protein
- Length
- 584 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine phosphatase yoph; Asp-ala-asp-glu-fty-leu-NH2
- EC
- 3.1.3.48
- Ligands
- NH2
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein-tyrosine phosphatase yoph (EC 3.1.3.48) | protein | 282 | 37% helix, 21% strand | — |
| C, E | Asp-ala-asp-glu-fty-leu-NH2 | protein | 4 | 0% helix, 0% strand | — |
| D, F | Asp-ala-asp-glu-fty-leu-NH2 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 4 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.52 | 0.78 | 23 | empty |
| 2 | 211 | 0.52 | 0.77 | 23 | empty |
| 3 | 241 | 0.48 | 0.74 | 37 | empty |
| 4 | 163 | 0.46 | 0.76 | 35 | empty |
| 5 | 120 | 0.42 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–F · 464 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 463 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 463 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 329 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 1QZ0 · Crystal Structure of the Yersinia Pestis Phosphatase YopH in Complex with a… · 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
- Elsewhere: RCSB PDB 1QZ0 · PDBe 1QZ0
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