Structure of PDB 6kmx Chain bB Binding Site BS05

Receptor Information
>6kmx Chain bB (length=727) Species: 1641165 (Halomicronema hongdechloris C2206) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATKFPKFSQDLQRDPTTRRLFYAIATAHDFESHDGMSEENLYQRIFASHF
GHLAIIFLWISGILFHVAWQGNFEQWIQDPLNNSPIAHAIWDAQFGPPAI
AAYTQAGAMNPVDICYSGVYHWWYTIGMRTNNDLFMGSIFLLLLSSVMLY
AGWLHLQPRFRPGLAWFKNAESRLNHHLAGLFGVSSLAWTGHLVHVALPE
SRGQHVGWDNFLSIRPHPEGLAPLFTGNWGAYAQNPDTAEHAFGTAQGAG
SAILTFLGGFHPQTESLWLTDMAHHHLAIAVIFIVAGHMYRTNFGIGHNI
KEMTEALQGGHKGIYDTYNNSLHFQLGWHLACLGVITSLVAQHMYAMPPY
AFMARDYTTMSALYTHHQYIAGFLMIGAFAHGAIFLIRDYDPEANRDNVL
ARMLAHKEAIISHLSWVSLFLGFHTLGLYVHNDCEVALGSPEKQILIEPV
FAQWTQAFHGKALYGINSLLSNPDSVASTAWPNYGNVWLSGWLEAVNNGA
NSLFLTIGPGDLLVHHAIALGLHVTTLILVKGALDARGSKLMPDKKDFGY
SFPCDGPGRGGTCDISAWDAFYLATFWMLNTLGWVTFYWHWKHLSVWSGN
VAQFNESSTYLMGWFRDYLWANSAQLINGYSPAGTNSLAVWAWMFLFGHL
AWAVSFMFLITWRGYWQELIETLMWAHENTPLSFGYPKDKPVALSIVQAR
LVGLTHFTVGYIATYGAFLIASTSSRF
Ligand information
Ligand IDF6C
InChIInChI=1S/C55H69N4O6.Mg/c1-12-38-35(8)42-27-46-39(13-2)41(30-60)47(57-46)28-43-36(9)40(52(58-43)50-51(55(63)64-11)54(62)49-37(10)44(59-53(49)50)29-45(38)56-42)23-24-48(61)65-26-25-34(7)22-16-21-33(6)20-15-19-32(5)18-14-17-31(3)4;/h13,25,27-33,51H,2,12,14-24,26H2,1,3-11H3,(H-,56,57,58,59,60,62);/q-1;+2/p-1/b34-25+,42-27-,43-28-,44-29-,45-29-,46-27-,47-28-,52-50-;/t32-,33-,51-;/m1./s1
InChIKeyYUTLCKLMRUVWDE-FOFJUSMOSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCc1c(c2n3c1C=C4C(=C5C(=O)C(C6=C7C(=C(C8=CC9=[N]([Mg]3(N87)[N]4=C65)C(=C2)C(=C9C=O)C=C)C)CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C(=O)OC)C)C
ACDLabs 12.01C(CC(=O)OC\C=C(/C)CCCC(C)CCCC(C)CCCC(C)C)C=9C=3N4C(=CC8=N5C(=Cc6c(C)c(CC)c7C=C1N(=C2C=3C(C(=O)C2=C1C)C(=O)OC)[Mg]45n67)C(/C=C)=C8C=O)C=9C
CACTVS 3.385CCc1c(C)c2C=C3N=C(C=C4[N@@]5[Mg]n2c1C=C6N=C7C(=C5C(=C4C)CCC(=O)OC\C=C(/C)CCC[C@H](C)CCC[C@H](C)CCCC(C)C)[C@@H](C(=O)OC)C(=O)C7=C6C)C(=C3C=C)C=O
CACTVS 3.385CCc1c(C)c2C=C3N=C(C=C4[N]5[Mg]n2c1C=C6N=C7C(=C5C(=C4C)CCC(=O)OCC=C(C)CCC[CH](C)CCC[CH](C)CCCC(C)C)[CH](C(=O)OC)C(=O)C7=C6C)C(=C3C=C)C=O
OpenEye OEToolkits 2.0.7CCc1c(c2n3c1C=C4C(=C5C(=O)[C@@H](C6=C7C(=C(C8=CC9=[N]([Mg]3(N87)[N]4=C65)C(=C2)C(=C9C=O)C=C)C)CCC(=O)OC/C=C(\C)/CCC[C@H](C)CCCC(C)CCCC(C)C)C(=O)OC)C)C
FormulaC55 H68 Mg N4 O6
NameChlorophyll F;
[methyl 9-ethenyl-14-ethyl-8-formyl-4,13,18-trimethyl-20-oxo-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,23,25-tetradehydro-24,26-dihydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]magnesium
ChEMBL
DrugBank
ZINC
PDB chain6kmx Chain bA Residue 844 [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]
PDB6kmx Structural basis for the adaptation and function of chlorophyll f in photosystem I.
Resolution2.41 Å
Binding residue
(original residue number in PDB)
L688 A691 H692 T695 S698 G700
Binding residue
(residue number reindexed from 1)
L673 A676 H677 T680 S683 G685
Annotation score1
Enzymatic activity
Enzyme Commision number 1.97.1.12: photosystem I.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0009055 electron transfer activity
GO:0016168 chlorophyll binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0015979 photosynthesis
Cellular Component
GO:0009522 photosystem I
GO:0009579 thylakoid
GO:0016020 membrane
GO:0031676 plasma membrane-derived thylakoid membrane
GO:0042651 thylakoid membrane

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6kmx, PDBe:6kmx, PDBj:6kmx
PDBsum6kmx
PubMed31932639
UniProtA0A1Z3HIL0

[Back to BioLiP]