Research workbench
Crystal structure of a trap periplasmic solute binding protein from bordetella bronchiseptica, target efi-510038 (BB2442), with bound (R)-mandelate and (S)-mandelate
Analyse Crystal structure of a trap periplasmic solute binding protein from bordetella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P56
- Type
- protein
- Length
- 947 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative extracellular solute-binding protein
- UniProt
- Q7WJQ1
- Ligands
- RMN, SMN
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative extracellular solute-binding protein | protein | 315 | 49% helix, 17% strand | Q7WJQ1 |
| B | Putative extracellular solute-binding protein | protein | 317 | 48% helix, 17% strand | Q7WJQ1 |
| C | Putative extracellular solute-binding protein | protein | 315 | 48% helix, 17% strand | Q7WJQ1 |
Ligands and binding sites
- RMN · (R)-mandelic acid · ligand · 2 copies · chains A, C
- SMN · (S)-mandelic acid · ligand · 2 copies · chains B, C
- PGE · Triethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.76 | 0.99 | 27 | RMN |
| 2 | 69 | 0.74 | 0.98 | 25 | RMN, SMN |
| 3 | 66 | 0.73 | 0.98 | 27 | SMN |
| 4 | 445 | 0.60 | 0.75 | 60 | empty |
| 5 | 78 | 0.40 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 518 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 438 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4P56 · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM BORDETELLA… · 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 Q7WJQ1
- Elsewhere: RCSB PDB 4P56 · PDBe 4P56 · UniProt Q7WJQ1
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