Research workbench
CWP6 from clostridium difficile
Analyse CWP6 from clostridium difficile in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J72
- Type
- protein
- Length
- 1,276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative N-acetylmuramoyl-L-alanine AMIDASE,AUTOLYSIN CWP6
- EC
- 3.5.1.28
- UniProt
- Q183L9
- Ligands
- CA, NA, ZN, CL
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative N-acetylmuramoyl-L-alanine AMIDASE,AUTOLYSIN CWP6 (EC 3.5.1.28) | protein | 638 | 36% helix, 28% strand | Q183L9 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.78 | 0.82 | 73 | CL |
| 2 | 507 | 0.71 | 0.80 | 41 | empty |
| 3 | 336 | 0.64 | 0.80 | 41 | empty |
| 4 | 308 | 0.55 | 0.76 | 45 | CA |
| 5 | 274 | 0.54 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2530 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5J72 · Cwp6 from Clostridium difficile · 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 Q183L9
- Elsewhere: RCSB PDB 5J72 · PDBe 5J72 · UniProt Q183L9
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