Research workbench
Crystal structure of the double mutant of pobr transcription factor inducer binding domain-3-hydroxy benzoic acid complex from acinetobacter
Analyse Crystal structure of the double mutant of pobr transcription factor inducer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HPI
- Type
- protein
- Length
- 691 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-hydroxybenzoate hydroxylase transcriptional activator
- UniProt
- Q43992
- Ligands
- 3HB, SO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P-hydroxybenzoate hydroxylase transcriptional activator | protein | 175 | 37% helix, 23% strand | Q43992 |
| B | P-hydroxybenzoate hydroxylase transcriptional activator | protein | 172 | 38% helix, 23% strand | Q43992 |
| C | P-hydroxybenzoate hydroxylase transcriptional activator | protein | 174 | 38% helix, 22% strand | Q43992 |
| D | P-hydroxybenzoate hydroxylase transcriptional activator | protein | 170 | 39% helix, 24% strand | Q43992 |
Ligands and binding sites
- 3HB · 3-hydroxybenzoic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.82 | 0.84 | 120 | empty |
| 2 | 95 | 0.77 | 0.98 | 24 | 3HB |
| 3 | 74 | 0.75 | 0.99 | 22 | 3HB |
| 4 | 87 | 0.74 | 0.97 | 22 | 3HB |
| 5 | 345 | 0.72 | 0.84 | 41 | empty |
Interfaces
5 interfaces between chains.
- C–D · 805 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 606 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 569 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 353 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 146 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 5HPI · Crystal Structure of the Double Mutant of PobR Transcription Factor Inducer Binding… · the same entry in another collection · chain D against D, TM-score 1.00
- Q43992 · AlphaFold monomer V2.0 prediction for P-hydroxybenzoate hydroxylase transcriptional… · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q43992
- Elsewhere: RCSB PDB 5HPI · PDBe 5HPI · UniProt Q43992
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