Research workbench
Crystal structure of D230A/H234A mutant of stationary phase survival protein (sure) from salmonella typhimurium
Analyse Crystal structure of D230A/H234A mutant of stationary phase survival protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GAD
- Type
- protein
- Length
- 489 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'/3'-nucleotidase sure
- EC
- 3.1.3.5, 3.1.3.6, 3.6.1.11
- UniProt
- P66881
- Ligands
- MG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11) | protein | 245 | 28% helix, 22% strand | P66881 |
| B | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11) | protein | 244 | 28% helix, 24% strand | P66881 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.66 | 0.79 | 49 | GOL |
| 2 | 379 | 0.63 | 0.78 | 42 | MG |
| 3 | 289 | 0.56 | 0.77 | 39 | MG |
| 4 | 62 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3373 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4GAD · Crystal Structure of D230A/H234A Mutant of Stationary Phase Survival Protein (SurE) from… · the same entry in another collection · chain A against A, TM-score 1.00
- P66881 · AlphaFold monomer V2.0 prediction for 5'/3'-nucleotidase sure (P66881) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P66881
- Elsewhere: RCSB PDB 4GAD · PDBe 4GAD · UniProt P66881
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