Research workbench
Structure of the cwld amidase from clostridioides difficile in complex with the gers lipoprotein
Analyse Structure of the cwld amidase from clostridioides difficile in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RAG
- Type
- protein
- Length
- 367 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein; Germination-specific N-acetylmuramoyl-L-alanine amidase, autolysin
- EC
- 3.5.1.28
- UniProt
- A0A031WJD5, Q18CJ4
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein | protein | 170 | 12% helix, 42% strand | A0A031WJD5 |
| B | Germination-specific N-acetylmuramoyl-L-alanine amidase, autolysin (EC 3.5.1.28) | protein | 197 | 43% helix, 19% strand | Q18CJ4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.72 | 0.80 | 63 | EDO |
| 2 | 95 | 0.46 | 0.80 | 21 | empty |
| 3 | 52 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1060 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 7RAG · Structure of the CwlD amidase from Clostridioides difficile in complex with the GerS… · 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 A0A031WJD5
- Every structure of UniProt Q18CJ4
- Elsewhere: RCSB PDB 7RAG · PDBe 7RAG · UniProt A0A031WJD5 · UniProt Q18CJ4
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