Research workbench
The active site of serratia endonuclease contains a conserved magnesium-water cluster
Analyse The active site of serratia endonuclease contains a conserved magnesium-water… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QAE
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (extracellular endonuclease)
- EC
- 3.1.30.2
- UniProt
- P13717
- Ligands
- MG
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (extracellular endonuclease) (EC 3.1.30.2) | protein | 240 | 27% helix, 22% strand | P13717 |
Ligands and binding sites
- MG · Magnesium ion · metal · 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 | 99 | 0.35 | 0.74 | 21 | MG |
| 2 | 79 | 0.32 | 0.74 | 19 | MG |
Interfaces
1 interface between chains.
- A–B · 930 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1QAE · The active site of serratia endonuclease contains a conserved magnesium-water cluster · the same entry in another collection · chain A against A, TM-score 1.00
- P13717 · AlphaFold monomer V2.0 prediction for nuclease (P13717) · 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 P13717
- Elsewhere: RCSB PDB 1QAE · PDBe 1QAE · UniProt P13717
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