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Stationary phase survival protein E (sure) from xylella fastidiosa

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: 5KSQ
Type: protein
Length: 509 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, PO4
Pockets: 9 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-nucleotidase sure (EC 3.1.3.5)	protein	252	28% helix, 27% strand	Q9PF20
B	5'-nucleotidase sure (EC 3.1.3.5)	protein	257	32% helix, 26% 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
PO4 · Phosphate ion · ion · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	351	0.69	0.83	59	MN, PO4
2	379	0.62	0.78	48	PO4
3	96	0.54	0.84	24	empty
4	104	0.51	0.82	28	empty
5	58	0.38	0.80	15	empty

Interfaces

1 interface between chains.

A–B · 3790 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

5KSQ · Stationary phase survival protein E (SurE) from Xylella fastidiosa · 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 0.88

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 5KSQ · PDBe 5KSQ · UniProt Q9PF20

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