Structure of PDB 8v9i Chain A

Receptor sequence

>8v9iA (length=595) Species: 1299 (Deinococcus radiodurans)

SDTPLLDQIHGPKDLKRLSREQLPALTEELRGEIVRVCSRGGLHLASSLG
AVDIITALHYVLDSPRDRILFDVGHQAYAHKILTGRRDQMADIKKEGGIS
GFTKVSESEHDAITVGHASTSLANALGMALARDAQGKDFHVAAVIGDGSL
TGGMALAALNTIGDMGRKMLIVLNDNEMSISENVGAMNKFMRGLQVQKWF
QAVEAVSKPSVNPFAAMGVRYVGPVDGHNVQELVWLLERLVDLDGPTILH
IVTTKGKGLSYAEADPIYWHGPAKFDPATGEYVPSSAYSWSAAFGEAVTE
WAKTDPRTFVVTPAMREGSGLVEFSRVHPHRYLDVGIAEEVAVTTAAGMA
LQGMRPVVAIYSTFLQRAYDQVLHDVAIEHLNVTFCIDRAGIVGADGATH
NGVFDLSFLRSIPGVRIGLPKDAAELRGMLKYAQTHDGPFAIRYPRGNTA
QVPAGTWPDLKWGEWERLKGGDDVVILAGGKALDYALKAAEDLPGVGVVN
ARFVKPLDEEMLREVGGRARALITVEDNTVVGGFGGAVLEALNSMNLHPT
VRVLGIPDEFQEHATAESVHARAGIDAPAIRTVLAELGVDVPIEV

3D structure

• PDB: 8v9i Potent Inhibition of E. coli DXP Synthase by a gem -Diaryl Bisubstrate Analog.
• Chain: A
• Resolution: 1.981 Å

Enzymatic activity

• Enzyme Commision number: 2.2.1.7: 1-deoxy-D-xylulose-5-phosphate synthase.

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	A1AAN	A	G49 L50 H51 S54 H82 A125 G153 D154 G155 S156 N183 M185 S186 I187 K289 H304 G305 M349 I371 E373 Y395 F398 R423 D430 H434 R480	G42 L43 H44 S47 H75 A118 G146 D147 G148 S149 N176 M178 S179 I180 K255 H270 G271 M315 I337 E339 Y361 F364 R389 D396 H400 R446
BS02	MG	A	D154 N183 M185	D147 N176 M178
BS03	BGQ	A	I187 I301	I180 I267

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0008661 1-deoxy-D-xylulose-5-phosphate synthase activity
• GO:0016740 transferase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding

Biological Process

• GO:0008299 isoprenoid biosynthetic process
• GO:0009228 thiamine biosynthetic process
• GO:0016114 terpenoid biosynthetic process
• GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
• GO:0052865 1-deoxy-D-xylulose 5-phosphate biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:8v9i, PDBe:8v9i, PDBj:8v9i
• PDBsum: 8v9i
• PubMed: 38513073
• UniProt: Q9RUB5|DXS_DEIRA 1-deoxy-D-xylulose-5-phosphate synthase (Gene Name=dxs)