Research workbench
Crystal structure of single chain pvuii
Analyse Crystal structure of single chain pvuii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KSK
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme pvuii
- EC
- 3.1.21.4
- UniProt
- P23657
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type-2 restriction enzyme pvuii (EC 3.1.21.4) | protein | 313 | 40% helix, 24% strand | P23657 |
| B | Type-2 restriction enzyme pvuii (EC 3.1.21.4) | protein | 311 | 40% helix, 24% strand | P23657 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
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 | 670 | 0.64 | 0.74 | 66 | empty |
| 2 | 223 | 0.47 | 0.74 | 40 | empty |
| 3 | 174 | 0.43 | 0.74 | 28 | SO4 |
| 4 | 112 | 0.41 | 0.76 | 25 | SO4 |
| 5 | 99 | 0.34 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 562 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 3KSK · PDBe 3KSK · UniProt P23657
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