Structure of PDB 2ivd Chain B

Receptor sequence

>2ivdB (length=449) Species: 34 (Myxococcus xanthus)

MNVAVVGGGISGLAVAHHLRSRGTDAVLLESSARLGGAVGTHALAGYLVE
QGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYVYTRGRLRSVPAS
PPAFLASDILPLGARLRVAGELFSRRAPEGVDESLAAFGRRHLGHRATQV
LLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGAIRAQKAQRQA
KLSGALSTFDGGLQVLIDALAASLGDAAHVGARVEGLAREDGGWRLIIEE
HGRRAELSVAQVVLAAPAHATAKLLRPLDDALAALVAGIAYAPIAVVHLG
FDAGTLPAPDGFGFLVPAEEQRRMLGAIHASTTFPFRAEGGRVLYSCMVG
GARQPGLVEQDEDALAALAREELKALAGVTARPSFTRVFRWPLGIPQYNL
GHLERVAAIDAALQRLPGLHLIGNAYKGVGLNDCIRNAAQLADALVAGN

3D structure

• PDB: 2ivd Crystal Structure of Protoporphyrinogen Oxidase from Myxococcus Xanthus and its Complex with the Inhibitor Acifluorfen.
• Chain: B
• Resolution: 2.3 Å

Enzymatic activity

• Enzyme Commision number: 1.3.3.4: protoporphyrinogen oxidase.

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	ACJ	B	R95 T166 G167 I168 F329 G330 F331 L332 A344 I345 M365 I412	R86 T157 G158 I159 F312 G313 F314 L315 A327 I328 M348 I395
BS02	FAD	B	V15 G16 G18 I19 S20 L38 E39 S40 G46 G61 P62 V251 P284 A287 N441 V446 G447 L448	V6 G7 G9 I10 S11 L29 E30 S31 G37 G52 P53 V234 P267 A270 N424 V429 G430 L431
BS03	TWN	B	R126 A128 G129 R134	R117 A119 G120 R125

Gene Ontology

Molecular Function

• GO:0004729 oxygen-dependent protoporphyrinogen oxidase activity
• GO:0016491 oxidoreductase activity

Biological Process

• GO:0006779 porphyrin-containing compound biosynthetic process
• GO:0006782 protoporphyrinogen IX biosynthetic process
• GO:0006783 heme biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005886 plasma membrane

External links

• PDB: RCSB:2ivd, PDBe:2ivd, PDBj:2ivd
• PDBsum: 2ivd
• PubMed: 17046834
• UniProt: P56601|PGOX_MYXXA Protoporphyrinogen oxidase (Gene Name=pgoX)