Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP

Structure of PDB 7drk Chain B Binding Site BS03

Receptor Information
>7drk Chain B (length=185) Species: 158879 (Staphylococcus aureus subsp. aureus N315) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNIPNQITVFRVVLIPVFILFALVDFGFGNVSFLGGYEIRIELLISGFIF
ILASLSDFVDGYLARKWNLVTNMGKFLDPLADKLLVASALIVLVQLGLTN
SVVAIIIIAREFAVTGLRLLQIEQGFVSAAGQLGKIKTAVTMVAITWLLL
GDPLATLIGLSLGQILLYIGVIFTILSGIEYFYKG
Ligand information
Ligand ID58A
InChIInChI=1S/C48H85N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-43(52)61-37-40(64-44(53)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2)38-62-67(57,58)66-68(59,60)63-39-41-45(54)46(55)47(65-41)51-36-35-42(49)50-48(51)56/h17-20,35-36,40-41,45-47,54-55H,3-16,21-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/b19-17+,20-18+/t40-,41-,45-,46-,47-/m1/s1
InChIKeyWVVFFOKRFKIBHD-ZIPNUMAKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCC=CCCCCCCCC(=O)OC[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N)OC(=O)CCCCCCCC=CCCCCCCCC
ACDLabs 12.01O=C1N(C=CC(=N1)N)C2OC(C(C2O)O)COP(=O)(O)OP(O)(OCC(COC(CCCCCCC\C=C\CCCCCCCC)=O)OC(CCCCCCCC=[C@H]CCCCCCCC)=O)=O
OpenEye OEToolkits 1.9.2CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)OC(=O)CCCCCCCC=CCCCCCCCC
OpenEye OEToolkits 1.9.2CCCCCCCCC=CCCCCCCCC(=O)OCC(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)OC(=O)CCCCCCCC=CCCCCCCCC
CACTVS 3.385CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N)OC(=O)CCCCCCC\C=C\CCCCCCCC
FormulaC48 H85 N3 O15 P2
Name5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine;
cytidinediphosphate-dioleoylglycerol;
CDP-1,2-dioleoyl-sn-glycerol
ChEMBL
DrugBank
ZINC
PDB chain7drk Chain B Residue 203 [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]
PDB7drk The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		P4 N5 I51 S54 D57 D60 G61 G74 K75 D78 K135 M142
Binding residue
(residue number reindexed from 1)		P4 N5 I51 S54 D57 D60 G61 G74 K75 D78 K135 M142
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.8.5: CDP-diacylglycerol--glycerol-3-phosphate 1-phosphatidyltransferase.
Gene Ontology
Molecular Function
GO:0008444 CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity
GO:0016740 transferase activity
GO:0016780 phosphotransferase activity, for other substituted phosphate groups
Biological Process
GO:0006655 phosphatidylglycerol biosynthetic process
GO:0008654 phospholipid biosynthetic process
GO:0046474 glycerophospholipid biosynthetic process
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:7drk, PDBe:7drk, PDBj:7drk
PDBsum7drk
PubMed34901881
UniProtP63756|PGSA_STAAN CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (Gene Name=pgsA)

[Back to BioLiP]

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417