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Crystal structure of a putative cell wall hydrolase (CD630_03720) from clostridium difficile 630 at 2.38 a resolution
Analyse Crystal structure of a putative cell wall hydrolase (CD630_03720) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HPE
- Type
- protein
- Length
- 1,735 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cell wall hydrolase TN916-LIKE,CTN1-ORF17
- UniProt
- Q18DB2
- Ligands
- CL
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Putative cell wall hydrolase TN916-LIKE,CTN1-ORF17 | protein | 289 | 46% helix, 13% strand | Q18DB2 |
| D | Putative cell wall hydrolase TN916-LIKE,CTN1-ORF17 | protein | 290 | 46% helix, 13% strand | Q18DB2 |
Ligands and binding sites
- CL · Chloride ion · ion · 9 copies · chains A, C, E, B, D, F
- GOL · Glycerol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.79 | 0.81 | 115 | CL |
| 2 | 555 | 0.69 | 0.79 | 83 | GOL |
| 3 | 114 | 0.64 | 0.88 | 30 | GOL |
| 4 | 298 | 0.55 | 0.76 | 33 | CL |
| 5 | 260 | 0.51 | 0.74 | 27 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1812 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 544 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 515 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 127 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered, oxidation).
Compared structures
- 4HPE · Crystal structure of a putative cell wall hydrolase (CD630_03720) from Clostridium… · 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 Q18DB2
- Elsewhere: RCSB PDB 4HPE · PDBe 4HPE · UniProt Q18DB2
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