Structure of PDB 4ydd Chain A

Receptor sequence

>4yddA (length=895) Species: 640081 (Azospira oryzae PS)

ISGAFEYSGWENFHRTQWSWDKKTRGAHLVNCTGACPHFVYSKDGVVMRE
EQSKDIAPMPNIPEYNPRGCNKGECGHDYMYGPHRIKYPLIRVGERGEGK
WRRATWEEALDMIADKCVDTIKNHAPDCISVYSPVPAVSPVSFSAGHRFA
HYIGAHAHTFYDWYGDHPTGQTQTCGVQGDTCETADWFNSKYIILWGSNP
TQTRIPDAHFLSEAQLNGAKIVSISPDYNSSTIKVDKWIHPQPGTDGALA
MAMAHVIIKEKLYDAHSLKEQTDLSYLVRSDTKRFLREADVVAGGSKDKF
YFWNAKTGKPVIPKGSWGDQPEKKGSPVGFLGRNTFAFPKGYIDLGDLDP
ALEGKFNMQLLDGKTVEVRPVFEILKSRLMADNTPEKAAKITGVTAKAIT
ELAREFATAKPSMIICGGGTQHWYYSDVLLRAMHLLTALTGTEGTNGGGM
NHYIGQWKPAFVAGLVALAFPEGVNKQRFCQTTIWTYIHAEVNDEIISSD
IDTEKYLRDSITTGQMPNMPEQGRDPKVFFVYRGNWLNQAKGQKYVLENL
WPKLELIVDINIRMDSTALYSDVVLPSAHWYEKLDLNVTSEHSYINMTEP
AIKPMWESKTDWQIFLALAKRVEMAAKRKKYEKFNDEKFKWVRDLSNLWN
QMTMDGKLAEDEAAAQYILDNAPQSKGITIQMLREKPQRFKSNWTSPLKE
GVPYTPFQYFVVDKKPWPTLTGRQQFYLDHDTFFDMGVELPTYKAPIDAD
KYPFRFNSPHSRHSVHSTFKDNVLMLRLQRGGPSIEMSPLDAKPLGIKDN
DWVEAWNNHGKVICRVKIRNGEQRGRVSMWHCPELYMDLLTGGSQSVCPV
RINPTNLVGNYGHLFFRPNYYGPAGSQRDVRVNVKRYIGATPISF

3D structure

• PDB: 4ydd Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.
• Chain: A
• Resolution: 1.86 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K76 P138 P140 W167 Y168 D170 P172 Y457 Q460
• Catalytic site (residue number reindexed from 1): K72 P134 P136 W163 Y164 D166 P168 Y453 Q456

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	SF4	A	H32 C36 G38 C40 G73 C74 G77	H28 C32 G34 C36 G69 C70 G73
BS02	MO	A	D170 G459	D166 G455
BS03	MGD	A	D170 G201 N203 Q206 T207 I228 S229 P230 D231 N233 D250 G421 G422 G423 W427 I458 G459 N761 P763 H764 S765 S768 V769 H770 R830 R882	D166 G197 N199 Q202 T203 I224 S225 P226 D227 N229 D246 G417 G418 G419 W423 I454 G455 N757 P759 H760 S761 S764 V765 H766 R826 R878
BS04	MD1	A	Y168 D170 H426 R537 G538 N539 Q543 I564 N565 I566 R567 D569 W584 D615 S762 H764 H770 S771 T772 H835 Q849 Q881	Y164 D166 H422 R533 G534 N535 Q539 I560 N561 I562 R563 D565 W580 D611 S758 H760 H766 S767 T768 H831 Q845 Q877

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0009061 anaerobic respiration
• GO:0045333 cellular respiration

Cellular Component

• GO:0016020 membrane
• GO:1990204 oxidoreductase complex

External links

• PDB: RCSB:4ydd, PDBe:4ydd, PDBj:4ydd
• PDBsum: 4ydd
• PubMed: 26940877
• UniProt: G8QM55