Structure of PDB 5xd8 Chain B

Receptor sequence

>5xd8B (length=367) Species: 1116375 (Vibrio sp. EJY3)

MKTTIKDIKTRLFKIPLKEILSDAKHGDHDHFELITTTVTLEDGSQGTGY
TYTGGKGGYSIKAMLEYDIQPALIGKDATQIEEIYDFMEWHIHYVGRGGI
STFAMSAVDIALWDLKGKREGLPLWKMAGGKNNTCKAYCGGIDLQFPLEK
LLNNICGYLESGFNAVKIKIGRENMQEDIDRIKAVRELIGPDITFMIDAN
YSLTVEQAIKLSKAVEQYDITWFEEPTLPDDYKGFAEIADNTAIPLAMGE
NLHTIHEFGYAMDQAKLGYCQPDASNCGGITGWLKAADLITEHNIPVCTH
GMQELHVSLVSAFDTGWLEVHSFPIDEYTKRPLVVENFRAVASNEPGIGV
EFDWDKIAQYEVHHHHH

3D structure

• PDB: 5xd8 Crystal structure analysis of 3,6-anhydro-l-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily
• Chain: B
• Resolution: 2.505 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): S22 T53 G140 K167 K169 D198 N200 E224 G249 E250 Q271 D273 H300 G301 M302 W317 E319 P324
• Catalytic site (residue number reindexed from 1): S22 T53 G140 K167 K169 D198 N200 E224 G249 E250 Q271 D273 H300 G301 M302 W317 E319 P324
• Enzyme Commision number: 5.5.1.25: 3,6-anhydro-L-galactonate cycloisomerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MG	B	D198 E224 E250	D198 E224 E250

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0016836 hydro-lyase activity
• GO:0016853 isomerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0016052 carbohydrate catabolic process
• GO:0019388 galactose catabolic process

External links

• PDB: RCSB:5xd8, PDBe:5xd8, PDBj:5xd8
• PDBsum: 5xd8
• PubMed: 28716734
• UniProt: H2IFX0|ACI_VIBSJ 3,6-anhydro-alpha-L-galactonate cycloisomerase (Gene Name=Vejaci)