MolNFT v1 · #103372 · protein
Crystal structure of a trap periplasmic solute binding protein from colwellia psychrerythraea (CPS_0129, target efi-510097) with bound calcium and pyruvate
4PET · Extracellular solute-binding protein, family 7: “Crystal structure of a trap periplasmic solute binding protein from colwellia psychrerythraea (CPS_0129…”. X-ray diffraction, 3 ligands (PYR, CA, CL), 5 pockets (best druggability…
- PDB
- 4PET
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein, family 7
- UniProt
- Q48AL6
- Ligands
- PYR, CA, CL
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular solute-binding protein, family 7 | protein | 329 | 54% helix, 15% strand | Q48AL6 |
| B | Extracellular solute-binding protein, family 7 | protein | 328 | 55% helix, 15% strand | Q48AL6 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.56 | 0.84 | 25 | empty |
| 2 | 105 | 0.52 | 0.82 | 23 | empty |
| 3 | 213 | 0.50 | 0.75 | 27 | empty |
| 4 | 178 | 0.50 | 0.77 | 26 | empty |
| 5 | 199 | 0.48 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2883 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 4PET · Crystal structure of a trap periplasmic solute binding protein from colwellia… · 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 Q48AL6
- Elsewhere: RCSB PDB 4PET · PDBe 4PET · UniProt Q48AL6
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