Structure of PDB 6q8w Chain D Binding Site BS01

Receptor Information
>6q8w Chain D (length=756) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVRVKVNDRIVEVPPGTSVMDAVFHAGYDVPLFCSEKHLSPIGACRMCLV
RIGLPIQWQPKLAASCVTAVADGMVVDTLSDVVREAQAGMVEFTLLNHPL
DCPTCDKGGACELQDRTVEYGLYEKYPLELPVYTRFEFTRRHVDKHHPLS
PFVILDRERCIHCKRCVRYFEEVPGDEVLDFIERGVHTFIGTMDFGLPSG
FSGNITDICPVGALLDLTARFRARNWEMEETPTTCALCPVGCGITADTRS
GELLRIRAREVPEVNEIWICDAGRFGHEWADQNRLKTPLVRKEGRLVEAT
WEEAFLALKEGLKEARGEEVGLYLAHDATLEEGLLASELAKALKTPHLDF
QGRTAAPASLFPPASLEDLLQADFALVLGDPTEEAPILHLRLSEFVRDLK
PPHRYNHGTPFADLQIKERMPRRTDKMALFAPYRAPLMKWAAIHEVHRPG
EEREILLALLGDKEGSEMVAKAKEAWEKAKNPVLILGAGVLQDTVAAERA
RLLAERKGAKVLAMTPAANARGLEAMGVLPGAKGASWDEPGALYAYYGFV
PPEEALKGKRFVVMHLSHLHPLAERYAHVVLPAPTFYEKRGHLVNLEGRV
LPLSPAPIENGEAEGALQVLALLAEALGVRPPFRLHLEAQKALKARKVPE
AMGRLSFRLKELRPKERKGAFYLRPTMWKAHQAVGKAQEAARAELWAHPE
TARAEALPEGAQVAVETPFGRVEARVVHREDVPKGHLYLSALGPAAGLRV
EGRVLV
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain6q8w Chain D Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6q8w Key role of quinone in the mechanism of respiratory complex I.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		H115 D118 C119 C122 C128 L130 Q131 R180 V232 G233
Binding residue
(residue number reindexed from 1)		H98 D101 C102 C105 C111 L113 Q114 R159 V211 G212
Annotation score1
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.-
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6q8w, PDBe:6q8w, PDBj:6q8w
PDBsum6q8w
PubMed32811817
UniProtQ56223|NQO3_THET8 NADH-quinone oxidoreductase subunit 3 (Gene Name=nqo3)

[Back to BioLiP]