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Crystal structure of a periplasmic solute binding protein (IPR025997) from streptobacillus moniliformis dsm-12112 (SMON_0317, target efi- 511281) with bound D-galactose
Analyse Crystal structure of a periplasmic 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
- 4Z0N
- Type
- protein
- Length
- 307 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding PROTEIN/LACI transcriptional regulator
- UniProt
- D1AWX5
- Ligands
- GAL, CA, NA, SO4
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 307 | 45% helix, 20% strand | D1AWX5 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- ACT · Acetate ion · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.44 | 0.77 | 19 | SO4 |
| 2 | 98 | 0.40 | 0.76 | 22 | empty |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4Z0N · Crystal Structure of a Periplasmic 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
- Every structure of UniProt D1AWX5
- Elsewhere: RCSB PDB 4Z0N · PDBe 4Z0N · UniProt D1AWX5
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