Research workbench
Stationary phase survival protein E (sure) from xylella fastidiosa - xfsure-ds (dimer smaller)
Analyse Stationary phase survival protein E (sure) from xylella fastidiosa - xfsure-ds… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KSS
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- 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, CL
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 252 | 26% helix, 27% strand | Q9PF20 |
| B | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 249 | 29% helix, 28% strand | Q9PF20 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 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 | 233 | 0.56 | 0.78 | 45 | IOD |
| 2 | 330 | 0.56 | 0.75 | 44 | MN, CL |
| 3 | 263 | 0.53 | 0.76 | 35 | CL |
| 4 | 50 | 0.34 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 3901 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5KSS · Stationary phase survival protein E (SurE) from Xylella fastidiosa - XFSurE-Ds (Dimer… · 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 B against A, TM-score 0.90
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 5KSS · PDBe 5KSS · UniProt Q9PF20
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.