Structure of PDB 6q8w Chain D

Receptor sequence

>6q8wD (length=756) Species: 300852 (Thermus thermophilus HB8)

MVRVKVNDRIVEVPPGTSVMDAVFHAGYDVPLFCSEKHLSPIGACRMCLV
RIGLPIQWQPKLAASCVTAVADGMVVDTLSDVVREAQAGMVEFTLLNHPL
DCPTCDKGGACELQDRTVEYGLYEKYPLELPVYTRFEFTRRHVDKHHPLS
PFVILDRERCIHCKRCVRYFEEVPGDEVLDFIERGVHTFIGTMDFGLPSG
FSGNITDICPVGALLDLTARFRARNWEMEETPTTCALCPVGCGITADTRS
GELLRIRAREVPEVNEIWICDAGRFGHEWADQNRLKTPLVRKEGRLVEAT
WEEAFLALKEGLKEARGEEVGLYLAHDATLEEGLLASELAKALKTPHLDF
QGRTAAPASLFPPASLEDLLQADFALVLGDPTEEAPILHLRLSEFVRDLK
PPHRYNHGTPFADLQIKERMPRRTDKMALFAPYRAPLMKWAAIHEVHRPG
EEREILLALLGDKEGSEMVAKAKEAWEKAKNPVLILGAGVLQDTVAAERA
RLLAERKGAKVLAMTPAANARGLEAMGVLPGAKGASWDEPGALYAYYGFV
PPEEALKGKRFVVMHLSHLHPLAERYAHVVLPAPTFYEKRGHLVNLEGRV
LPLSPAPIENGEAEGALQVLALLAEALGVRPPFRLHLEAQKALKARKVPE
AMGRLSFRLKELRPKERKGAFYLRPTMWKAHQAVGKAQEAARAELWAHPE
TARAEALPEGAQVAVETPFGRVEARVVHREDVPKGHLYLSALGPAAGLRV
EGRVLV

3D structure

• PDB: 6q8w Key role of quinone in the mechanism of respiratory complex I.
• Chain: D
• Resolution: 3.4 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): A293 A376 A377 A509 P537 A538
• Catalytic site (residue number reindexed from 1): A272 A355 A356 A488 P516 A517
• Enzyme Commision number: 7.1.1.-

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	D	H115 D118 C119 C122 C128 L130 Q131 R180 V232 G233	H98 D101 C102 C105 C111 L113 Q114 R159 V211 G212
BS02	SF4	D	C181 I182 C184 C187 C230 V232 L235	C160 I161 C163 C166 C209 V211 L214
BS03	SF4	D	C256 C259 V261 G262 C263 I290 C291 P407 I408	C235 C238 V240 G241 C242 I269 C270 P386 I387
BS04	FES	D	C34 G43 C45 R46 C48 C83	C34 G43 C45 R46 C48 C66

Gene Ontology

Molecular Function

• GO:0003954 NADH dehydrogenase activity
• GO:0008137 NADH dehydrogenase (ubiquinone) activity
• GO:0016491 oxidoreductase activity
• GO:0016651 oxidoreductase activity, acting on NAD(P)H
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0048038 quinone binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051537 2 iron, 2 sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0042773 ATP synthesis coupled electron transport
• GO:0045333 cellular respiration
• GO:1902600 proton transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:6q8w, PDBe:6q8w, PDBj:6q8w
• PDBsum: 6q8w
• PubMed: 32811817
• UniProt: Q56223|NQO3_THET8 NADH-quinone oxidoreductase subunit 3 (Gene Name=nqo3)