Structure of PDB 4ydd Chain E

Receptor sequence

>4yddE (length=892) Species: 640081 (Azospira oryzae PS)

AFEYSGWENFHRTQWSWDKKTRGAHLVNCTGACPHFVYSKDGVVMREEQS
KDIAPMPNIPEYNPRGCNKGECGHDYMYGPHRIKYPLIRVGERGEGKWRR
ATWEEALDMIADKCVDTIKNHAPDCISVYSPVPAVSPVSFSAGHRFAHYI
GAHAHTFYDWYGDHPTGQTQTCGVQGDTCETADWFNSKYIILWGSNPTQT
RIPDAHFLSEAQLNGAKIVSISPDYNSSTIKVDKWIHPQPGTDGALAMAM
AHVIIKEKLYDAHSLKEQTDLSYLVRSDTKRFLREADVVAGGSKDKFYFW
NAKTGKPVIPKGSWGDQPEKKGSPVGFLGRNTFAFPKGYIDLGDLDPALE
GKFNMQLLDGKTVEVRPVFEILKSRLMADNTPEKAAKITGVTAKAITELA
REFATAKPSMIICGGGTQHWYYSDVLLRAMHLLTALTGTEGTNGGGMNHY
IGQWKPAFVAGLVALAFPEGVNKQRFCQTTIWTYIHAEVNDEIISSDIDT
EKYLRDSITTGQMPNMPEQGRDPKVFFVYRGNWLNQAKGQKYVLENLWPK
LELIVDINIRMDSTALYSDVVLPSAHWYEKLDLNVTSEHSYINMTEPAIK
PMWESKTDWQIFLALAKRVEMAAKRKKYEKFNDEKFKWVRDLSNLWNQMT
MDGKLAEDEAAAQYILDNAPQSKGITIQMLREKPQRFKSNWTSPLKEGVP
YTPFQYFVVDKKPWPTLTGRQQFYLDHDTFFDMGVELPTYKAPIDADKYP
FRFNSPHSRHSVHSTFKDNVLMLRLQRGGPSIEMSPLDAKPLGIKDNDWV
EAWNNHGKVICRVKIRNGEQRGRVSMWHCPELYMDLLTGGSQSVCPVRIN
PTNLVGNYGHLFFRPNYYGPAGSQRDVRVNVKRYIGATPISF

3D structure

• PDB: 4ydd Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.
• Chain: E
• 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): K69 P131 P133 W160 Y161 D163 P165 Y450 Q453

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	E	H32 C36 G38 C40 G73 C74 G77	H25 C29 G31 C33 G66 C67 G70
BS02	MO	E	D170 G459	D163 G452
BS03	MGD	E	D170 G201 N203 Q206 T207 I228 P230 N233 G248 D250 G421 G422 G423 W427 I458 G459 N761 P763 H764 S765 S768 V769 H770 R830 R882	D163 G194 N196 Q199 T200 I221 P223 N226 G241 D243 G414 G415 G416 W420 I451 G452 N754 P756 H757 S758 S761 V762 H763 R823 R875
BS04	MD1	E	Y168 D170 H426 R537 G538 N539 Q543 I564 N565 R567 D569 S581 K587 D615 S762 H764 H770 S771 T772 H835 Q849 Q881	Y161 D163 H419 R530 G531 N532 Q536 I557 N558 R560 D562 S574 K580 D608 S755 H757 H763 S764 T765 H828 Q842 Q874

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