Structure of PDB 6ldk Chain A Binding Site BS01

Receptor Information
>6ldk Chain A (length=813) Species: 237561 (Candida albicans SC5314) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FSFPKEEEAVIKHWDDVNAFQRTLELTEDLPPFAFFDGPPFATGTPHYGH
ILASTVKDIIPRYATMNGYHVERRFGWDTHGLPVEHEIDKKLNITSKEDV
YAMGIDKYNAECRAIVMRYADEWRRTIKRLGRWIDMDNDYKTLYPEFMES
VWWAFKELFNKDAVYRGLRVMPYSTACTTPLSNFEAQQNYKEVNDPALTI
SFPLLDNEDTCLVAWTTTPWTLPANLALAVNPKFEYVKIFDEEKKKNFIL
LESLISTLYKKPKSAKFKVVEKILGKDLVGLKYKPLFNYFYEDFKDTGFR
VIPADYVTNDSGTGIVHQAPSYGEEDFNSTKAAGVINKKLPPSIVDDSGR
MESNVPEIAGMYFKDADKVIIKKLSEEGRLLVNTQVKHSYPFCWRSDTPL
MYRTVPAWFVRIGEVIPEMLDNVEKTNWVPSNIKDKRFSNWIANARDWNI
SRNRYWGTPIPLWVSDDFEEMVCVGSIQELRELSGRDDITDIHRESIDSI
TIPSKKGKGQLKRIEEVFDCWFESGSMPYASKHYPFENEKKFLDAFPANF
ISEGLDQTRGWFYTLTVLGTHLFKTAPYQNVIVTGIVLAADGKKMSKRLK
NYPDPTLVLEKYGADALRLYLINSPVLRAETLKFKEEGVKEIVSSVLLPW
YNSYKFLKDAADLFKKDNGKDFVYDNSLHSTNVMDRWLLASIQSLIKFIH
EEMTGYRLYTVVPRLLHFIDDLTNWYIRFNRRRIKGYASEDVEDTQKGLN
TLVEALLTLSRAMAPFTPYLADGIYQRIKVYFKQEDLEKIAINPKNVDLR
SVHFLSYPSVRQE
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain6ldk 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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PDB6ldk Structural Basis for the Antibiotic Resistance of Eukaryotic Isoleucyl-tRNA Synthetase.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		F55 H61 G63 H64 E568 G569 D571 I601 V602
Binding residue
(residue number reindexed from 1)		F41 H47 G49 H50 E553 G554 D556 I586 V587
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) P53 D92 W536 Q572 W576 K609 K612
Catalytic site (residue number reindexed from 1) P39 D78 W521 Q557 W561 K594 K597
Enzyme Commision number 6.1.1.5: isoleucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004822 isoleucine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006428 isoleucyl-tRNA aminoacylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6ldk, PDBe:6ldk, PDBj:6ldk
PDBsum6ldk
PubMed32088946
UniProtQ59RI1

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