Research workbench
Structural Genomics, the crystal structure of the C-terminal domain of histidine utilization repressor from Pseudomonas syringae pv. tomato str. DC3000
Analyse Structural Genomics, the crystal structure of the C-terminal domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PKH
- Type
- protein
- Length
- 1,132 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Pseudomonas syringae pv. tomato
- Molecule
- Histidine utilization repressor
- UniProt
- Q87UX0
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.95 · 2 distinct chains · 19% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, G | Histidine utilization repressor | protein | 141 | 21% helix, 50% strand | Q87UX0 |
| B, C, E, H | Histidine utilization repressor | protein | 142 | 18% helix, 51% strand | Q87UX0 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 32 copies · chains A, B, E, C, D, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.82 | 0.84 | 106 | EDO |
| 2 | 625 | 0.78 | 0.84 | 70 | EDO |
| 3 | 323 | 0.74 | 0.87 | 42 | EDO |
| 4 | 350 | 0.74 | 0.86 | 49 | empty |
| 5 | 94 | 0.62 | 0.89 | 27 | empty |
Interfaces
20 interfaces between chains.
- E–F · 1286 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1286 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1272 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1257 Ų buried · 24 hydrogen bonds · protein-protein
- C–G · 583 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2PKH · Structural genomics, the crystal structure of the C-terminal domain of histidine… · 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 Q87UX0
- Elsewhere: RCSB PDB 2PKH · PDBe 2PKH · UniProt Q87UX0
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