MolNFT v1 · #104316 · protein
Crystal structure of periplasmic binding protein type 1 from bordetella pertussis tohama I complexed with 3-hydroxy benzoic acid
4Q6W · Putative LEU/ILE/VAL-binding protein: “Crystal structure of periplasmic binding protein type 1 from bordetella pertussis tohama I complexed with…”. X-ray diffraction, 2 ligands (3HB, SO4), 12 pockets (best druggability 0.66). MolNFT…
- PDB
- 4Q6W
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative LEU/ILE/VAL-binding protein
- UniProt
- Q7VS30
- Ligands
- 3HB, SO4
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative LEU/ILE/VAL-binding protein | protein | 376 | 44% helix, 19% strand | Q7VS30 |
| B | Putative LEU/ILE/VAL-binding protein | protein | 376 | 44% helix, 19% strand | Q7VS30 |
Ligands and binding sites
- 3HB · 3-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.66 | 0.86 | 34 | empty |
| 2 | 59 | 0.64 | 0.93 | 18 | 3HB |
| 3 | 57 | 0.63 | 0.93 | 18 | 3HB |
| 4 | 235 | 0.58 | 0.79 | 30 | empty |
| 5 | 99 | 0.55 | 0.84 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4Q6W · Crystal Structure of Periplasmic Binding Protein type 1 from Bordetella pertussis Tohama… · 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 Q7VS30
- Elsewhere: RCSB PDB 4Q6W · PDBe 4Q6W · UniProt Q7VS30
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