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Crystal structure of E112A/H234A mutant of stationary phase survival protein (sure) from salmonella typhimurium co-crystallized and soaked with AMP.

Analyse Crystal structure of E112A/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: 4XGP
Type: protein
Length: 1,030 residues
Chains: 4
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: ADE, MG, PO4
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 26% 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	264	29% helix, 26% strand	P66881
B	5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11)	protein	257	29% helix, 26% strand	P66881
C	5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11)	protein	255	30% helix, 26% strand	P66881
D	5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11)	protein	254	29% helix, 27% strand	P66881

Ligands and binding sites

ADE · Adenine · ligand · chains A, B
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · chains A
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1141	0.83	0.85	100	empty
2	700	0.75	0.81	67	MG, EDO
3	285	0.75	0.88	38	PO4, ADE
4	471	0.73	0.83	45	MG, EDO
5	455	0.72	0.82	44	MG, EDO

Interfaces

6 interfaces between chains.

C–D · 3905 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 3860 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 523 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 511 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 507 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4XGP · Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (SurE) from… · the same entry in another collection · chain C against C, TM-score 1.00
P66881 · AlphaFold monomer V2.0 prediction for 5'/3'-nucleotidase sure (P66881) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 4XGP · PDBe 4XGP · UniProt P66881

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