Structure of PDB 6tg9 Chain F Binding Site BS03

Receptor Information
>6tg9 Chain F (length=493) Species: 1415161 (Rhodobacter capsulatus Y262) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIWLPCDAAAKACGAEAVLAALRLEAEKRGGALDIARNGSRGMIWLEPL
LEVETPAGRIGFGPMTPADVPALFDALESHPKALGLVEEIPFFKRQTRLT
FARCGRIEPLSLAQFAAAEGWAGLRKALKMTPAEVVEEVLASGLRGRGGA
GFPTGIKWRTVAAAQADQKYIVCNVDEGDSGSFADRMLIEGDPFCLVEGM
AIAGHAVGATRGYVYIRSEYPDAIAVMRAAIAMAKPFLAEAGFEMEVRVG
AGAYVCGEETSLLNSLEGKRGTVRAKPPLPALKGLFGKPTVVNNLLSLAA
VPWIIAHGAKAYESFGMDRSRGTIPLQIGGNVKRGGLFETGFGITLGELV
EDICGGTASGRPVKAVQVGGPLGAYHPVSDYHLPFCYEQFAGQGGLVGHA
GLVVHDDTADMLKLARFAMEFCAIESCGTCTPCRIGAVRGVEVIDRIAAG
DASAMPLLDDLCQTMKLGSLCALGGFTPYPVQSAIRHFPADFP
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain6tg9 Chain F Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6tg9 Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase.
Resolution3.24 Å
Binding residue
(original residue number in PDB)		F152 K157 E258 E259 L279 K466 L470
Binding residue
(residue number reindexed from 1)		F152 K157 E258 E259 L279 K466 L470
Annotation score4
Enzymatic activity
Enzyme Commision number 1.2.1.2: Transferred entry: 1.17.1.9.
Gene Ontology
Molecular Function
GO:0008137 NADH dehydrogenase (ubiquinone) activity
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:1902600 proton transmembrane transport

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6tg9, PDBe:6tg9, PDBj:6tg9
PDBsum6tg9
PubMed32313256
UniProtD5AQH1

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