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Crystal structure of the pvuii endonuclease with PR3+ and SO4 ions bound in the active site at 2.05A.
Analyse Crystal structure of the pvuii endonuclease with PR3+ and SO4 ions bound in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K0Z
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II restriction enzyme pvuii
- EC
- 3.1.21.4
- UniProt
- P23657
- Ligands
- PR, SO4
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II restriction enzyme pvuii (EC 3.1.21.4) | protein | 151 | 42% helix, 23% strand | P23657 |
| B | Type II restriction enzyme pvuii (EC 3.1.21.4) | protein | 154 | 40% helix, 23% strand | P23657 |
Ligands and binding sites
- PR · Praseodymium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.45 | 0.74 | 30 | empty |
| 2 | 94 | 0.39 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1541 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1K0Z · Crystal Structure of the PvuII endonuclease with Pr3+ and SO4 ions bound in the active… · the same entry in another collection · chain A against A, TM-score 1.00
- P23657 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme pvuii (P23657) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P23657
- Elsewhere: RCSB PDB 1K0Z · PDBe 1K0Z · UniProt P23657
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