Research workbench
Stationary phase survival protein E (sure) from xylella fastidiosa- xfsure-tsamp (tetramer smaller - crystallization with 3'AMP).
Analyse Stationary phase survival protein E (sure) from xylella fastidiosa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KST
- Type
- protein
- Length
- 1,023 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-nucleotidase sure
- EC
- 3.1.3.5
- UniProt
- Q9PF20
- Ligands
- MN, IOD, PO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 257 | 29% helix, 28% strand | Q9PF20 |
| C | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 254 | 30% helix, 28% strand | Q9PF20 |
| D | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 255 | 30% helix, 28% strand | Q9PF20 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- IOD · Iodide ion · ion · 6 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.72 | 0.86 | 53 | PO4 |
| 2 | 273 | 0.70 | 0.85 | 58 | PO4 |
| 3 | 196 | 0.66 | 0.86 | 32 | PO4 |
| 4 | 70 | 0.46 | 0.83 | 27 | empty |
| 5 | 73 | 0.45 | 0.82 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4109 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 3927 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 701 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 631 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 571 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5KST · Stationary phase Survival protein E (SurE) from Xylella fastidiosa- XfSurE-TSAmp… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PF20 · AlphaFold monomer V2.0 prediction for 5'-nucleotidase sure (Q9PF20) · a predicted model of the same protein · chain C against A, TM-score 0.89
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 Q9PF20
- Elsewhere: RCSB PDB 5KST · PDBe 5KST · UniProt Q9PF20
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