Structure of PDB 4xpd Chain A Binding Site BS01

Receptor Information
>4xpd Chain A (length=774) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DQFLEALKLYEGKQYKKSLKLLDAILKKDGSHVDSLALKGLDLYSVGEKD
DAASYVANAIRKISPICCHVLGIYMRNTKEYKESIKWFTAALNNGSTNKQ
IYRDLATLQSQIGDFKNALVSRKKYWEAFLGYRANWTSLAVAQDVNGERQ
QAINTLSQFEKLAEGKISDSEKYEHSECLMYKNDIMYKAASDNQDKLQNV
LKHLNDIEPCVFDKFGLLERKATIYMKLGQLKDASIVYRTLIKRNPDNFK
YYKLLEVSLGIQGDNKLKKALYGKLEQFYPRCEPPKFIPLTFLQDKEELS
KKLREYVLPQLERGVPATFSNVKPLYQRRKSKVSPLLEKIVLDYLSGLDP
TQDPIPFIWTNYYLSQHFLFLKDFPKAQEYIDAALDHTPTLVEFYILKAR
ILKHLGLMDTAAGILEEGRQLDLQDRFINCKTVKYFLRANNIDKAVEVAS
LFTKNDDSVNGIKDLHLVEASWFIVEQAEAYYRLYLDRKKKLDDLASLKK
QIANDIKENQWLVRKYKGLALKRFNAIPKFYKQFEDDQLDFHSYCMRKGT
PRAYLEMLEWGKALYTKPMYVRAMKEASKLYFQMHDDRLKKRKETEAKSV
AAYPSDQDNDVFGEKLIETSTPMEDFATEFYNNYSMQVREDERDYILDFE
FNYRIGKLALCFASLNKFAKRFGTTSGLFGSMAIVLLHATRNDTPFVVTK
SLEKEYSENFPLNEFDWLNFYQEKFGKNDINGLLFLYRYRDDVPIGSSNL
KEMIISSLSPLEPHSQNEILQYYL
Ligand information
Ligand IDG4P
InChIInChI=1S/C10H17N5O17P4/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(30-36(26,27)32-34(21,22)23)3(29-9)1-28-35(24,25)31-33(18,19)20/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyBUFLLCUFNHESEH-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O[P@@](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H17 N5 O17 P4
NameGUANOSINE-5',3'-TETRAPHOSPHATE;
guanosine tetraphosphate;
ppGpp
ChEMBL
DrugBankDB04022
ZINCZINC000008217069
PDB chain4xpd Chain A Residue 901 [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)		K349 Q353 R426 K429 K457 K460
Binding residue
(residue number reindexed from 1)		K323 Q327 R400 K403 K431 K434
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004596 peptide alpha-N-acetyltransferase activity
GO:0005515 protein binding
GO:0043022 ribosome binding
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0031415 NatA complex

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:4xpd, PDBe:4xpd, PDBj:4xpd
PDBsum4xpd
PubMed
UniProtP12945|NAT1_YEAST N-terminal acetyltransferase A complex subunit NAT1 (Gene Name=NAT1)

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