Research workbench
Crystal structure of a TRAP transporter solute binding protein (IPR025997) from Bordetella bronchiseptica RB50 (BB0280, TARGET EFI-500035) mixed occupancy dimer, copurified calcium and picolinate bound active site versus apo site
Analyse Crystal structure of a TRAP transporter solute binding protein (IPR025997) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YZZ
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.3
- Source
- BORDETELLA BRONCHISEPTICA
- Molecule
- Trap transporter solute binding protein
- Ligands
- 6PC, CA
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.3 · 1 distinct chain · 56% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Trap transporter solute binding protein | protein | 336 | 56% helix, 16% strand | — |
Ligands and binding sites
- 6PC · Pyridine-2-carboxylic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.73 | 0.97 | 23 | CA, 6PC |
| 2 | 64 | 0.73 | 0.98 | 18 | PEG |
| 3 | 372 | 0.67 | 0.80 | 40 | NHE |
| 4 | 72 | 0.41 | 0.80 | 15 | empty |
| 5 | 65 | 0.40 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–D · 3543 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4YZZ · Crystal structure of a trap transporter solute binding protein (IPR025997) from… · 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 4YZZ · PDBe 4YZZ
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