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2.05 Angstrom Resolution Crystal Structure of Peptidoglycan-Binding Protein from Clostridioides difficile in Complex with Glutamine Hydroxamate.
Analyse 2.05 Angstrom Resolution Crystal Structure of Peptidoglycan-Binding Protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TV7
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Peptoclostridium difficile (strain 630)
- Molecule
- Putative peptidoglycan-binding/hydrolysing protein
- UniProt
- Q181X4
- Ligands
- HGA
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · resolution 2.05 · 1 distinct chain · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative peptidoglycan-binding/hydrolysing protein | protein | 158 | 35% helix, 23% strand | Q181X4 |
Ligands and binding sites
- HGA · Glutamine hydroxamate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.51 | 0.82 | 25 | empty |
| 2 | 88 | 0.48 | 0.82 | 25 | empty |
| 3 | 75 | 0.36 | 0.76 | 20 | empty |
| 4 | 86 | 0.33 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 437 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered, artifact).
Compared structures
- 5TV7 · 2.05 ångström resolution crystal structure of peptidoglycan-binding protein 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 Q181X4
- Elsewhere: RCSB PDB 5TV7 · PDBe 5TV7 · UniProt Q181X4
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