Structure of PDB 4xpd Chain B Binding Site BS03

Receptor Information
>4xpd Chain B (length=187) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PINIRRATINDIICMQNANLHNLPENYMMKYYMYHILSWPEASFVATTTT
LDPTYLAPGEKLVGYVLVKMNDDQNEPPNGHITSLSVMRTYRRMGIAENL
MRQALFALREVHQAEYVSLHVRQSNRAALHLYRDTLAFEVLSIEKSYYQD
GEDAYAMKKVLKLEELQISNFTHRRKLEDDLESDLLE
Ligand information
Ligand IDCMC
InChIInChI=1S/C23H38N7O18P3S/c1-23(2,18(35)21(36)26-4-3-13(31)25-5-6-52-8-14(32)33)9-45-51(42,43)48-50(40,41)44-7-12-17(47-49(37,38)39)16(34)22(46-12)30-11-29-15-19(24)27-10-28-20(15)30/h10-12,16-18,22,34-35H,3-9H2,1-2H3,(H,25,31)(H,26,36)(H,32,33)(H,40,41)(H,42,43)(H2,24,27,28)(H2,37,38,39)/t12-,16-,17-,18+,22-/m1/s1
InChIKeyOBUOSIHPWVNVJN-GRFIIANRSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)CSCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSCC(O)=O
OpenEye OEToolkits 1.7.2CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSCC(=O)O)O
OpenEye OEToolkits 1.7.2CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSCC(=O)O)O
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSCC(O)=O
FormulaC23 H38 N7 O18 P3 S
NameCARBOXYMETHYL COENZYME *A
ChEMBL
DrugBank
ZINCZINC000085534448
PDB chain4xpd Chain F Residue 101 [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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PDB4xpd Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate
Resolution2.81 Å
Binding residue
(original residue number in PDB)		L24 S117 L118 S119 V120 R125 R126 M127 G128 A130 H153 V154 N158 A160 A161 H163 Y165 T168
Binding residue
(residue number reindexed from 1)		L23 S84 L85 S86 V87 R92 R93 M94 G95 A97 H120 V121 N125 A127 A128 H130 Y132 T135
Annotation score3
Enzymatic activity
Enzyme Commision number 2.3.1.255: N-terminal amino-acid N(alpha)-acetyltransferase NatA.
Gene Ontology
Molecular Function
GO:0004596 peptide alpha-N-acetyltransferase activity
GO:0005515 protein binding
GO:0016746 acyltransferase activity
GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
GO:0042802 identical protein binding
GO:1990189 peptide-serine-alpha-N-acetyltransferase activity
GO:1990190 peptide-glutamate-alpha-N-acetyltransferase activity
Biological Process
GO:0006474 N-terminal protein amino acid acetylation
Cellular Component
GO:0005737 cytoplasm
GO:0031415 NatA complex

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4xpd, PDBe:4xpd, PDBj:4xpd
PDBsum4xpd
PubMed
UniProtP07347|ARD1_YEAST N-terminal acetyltransferase A complex catalytic subunit ARD1 (Gene Name=ARD1)

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