Structure of PDB 1ker Chain B

Receptor sequence

>1kerB (length=347) Species: 1307 (Streptococcus suis)

SQFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAI
LGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHT
NFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTA
ETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKF
IPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYL
IGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDE
LGWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK

3D structure

• PDB: 1ker Toward a structural understanding of the dehydratase mechanism.
• Chain: B
• Resolution: 2.2 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): T125 D126 E127 Y161 K165
• Catalytic site (residue number reindexed from 1): T124 D125 E126 Y160 K164
• Enzyme Commision number: 4.2.1.46: dTDP-glucose 4,6-dehydratase.

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	DAU	B	S86 N88 T125 D126 E127 Y161 N190 K200 F201 R204 Q205 K216 L217 Y218 R225 N260 R284 H287	S85 N87 T124 D125 E126 Y160 N189 K199 F200 R203 Q204 K215 L216 Y217 R224 N259 R283 H286
BS02	NAD	B	G14 F15 I16 D37 K38 L39 T40 G43 D62 I63 Y82 A83 A84 S86 T101 S124 T125 Y161 K165 C188 N191	G13 F14 I15 D36 K37 L38 T39 G42 D61 I62 Y81 A82 A83 S85 T100 S123 T124 Y160 K164 C187 N190

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008460 dTDP-glucose 4,6-dehydratase activity
• GO:0016829 lyase activity

Biological Process

• GO:0009225 nucleotide-sugar metabolic process

External links

• PDB: RCSB:1ker, PDBe:1ker, PDBj:1ker
• PDBsum: 1ker
• PubMed: 11796113
• UniProt: Q8GIP9