Research workbench
Crystal structure of putative haloacid dehalogenase-like hydrolase (YP_001086940.1) from clostridium difficile 630 at 2.10 a resolution
Analyse Crystal structure of putative haloacid dehalogenase-like hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FZQ
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hydrolase
- UniProt
- Q188R2
- Ligands
- NA, PO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative hydrolase | protein | 271 | 38% helix, 24% strand | Q188R2 |
| B | Putative hydrolase | protein | 258 | 37% helix, 25% strand | Q188R2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.75 | 0.78 | 110 | PO4, NA |
| 2 | 93 | 0.42 | 0.78 | 20 | empty |
| 3 | 87 | 0.36 | 0.75 | 18 | empty |
| 4 | 58 | 0.32 | 0.77 | 15 | EDO |
| 5 | 55 | 0.31 | 0.76 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 1112 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 3FZQ · Crystal structure of putative haloacid dehalogenase-like hydrolase (YP_001086940.1) 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 Q188R2
- Elsewhere: RCSB PDB 3FZQ · PDBe 3FZQ · UniProt Q188R2
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