Research workbench
The structure of potential metal-dependent hydrolase with cyclase activity
Analyse The structure of potential metal-dependent hydrolase with cyclase activity in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KRV
- Type
- protein
- Length
- 402 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase
- UniProt
- P84132
- Ligands
- ZN, CL, SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase | protein | 201 | 17% helix, 34% strand | P84132 |
| B | Hydrolase | protein | 201 | 21% helix, 30% strand | P84132 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
- CL · Chloride ion · ion · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.64 | 0.84 | 30 | CL |
| 2 | 110 | 0.63 | 0.88 | 22 | EDO |
| 3 | 185 | 0.58 | 0.81 | 31 | empty |
| 4 | 227 | 0.54 | 0.77 | 35 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2283 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 3KRV · The Structure Of Potential Metal-Dependent Hydrolase With Cyclase Activity · the same entry in another collection · chain A against A, TM-score 1.00
- 1R61 · The structure of predicted metal-dependent hydrolase from Bacillus stearothermophilus · a predicted model of the same protein · chain A against A, TM-score 1.00
- 1R61 · The structure of predicted metal-dependent hydrolase from bacillus stearothermophilus · a predicted model of the same protein · 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 P84132
- Elsewhere: RCSB PDB 3KRV · PDBe 3KRV · UniProt P84132
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