Structure of PDB 6nab Chain A Binding Site BS01

Receptor Information
>6nab Chain A (length=496) Species: 5763 (Naegleria fowleri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EGIDVKKQENFSEWYSQVITKSEFLDYYDVSGCYIFRPNCWFVWESVQKF
FDAEIKKLGVQNVMFPLFVTKRALETEKDHVEGFSPEVAWVTKSGNSDLQ
EPIALRPTSETIMYPSYAKWIQSHRDLPLKLNQWTNVVRWEFKHAVPFIR
SREFYWQEGHSAFKSKEEADEEVFTILELYKRVYEELLAVPVIKGTKTEN
EKFAGADYTTTVETFIATNGRAVQGGTSHHLGQNFSKMFKIQFEAENKET
QFAYQNSWGLSTRTLGVMIMVHGDDKGMVLPPRVAFCQVVVIPLIDNATL
VEKTKEIYNELEKAGIRVKLDDRRTPGWKYNYWELRGVPLRIEVGPKDLE
KQQIMLCRRDTGEKWTMPLSEFSGDSIKAVLDKIHDSMLNKARKEMNERI
VVTRTWPEFIKALNSGNMCLIPWHESKAAEEYIKEKSKLESVQSQSDANT
GLTGAAKSLCVPLDQSSFPSLEGLENFYPEEAHKKPNCWALFGRSY
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 chain6nab Chain A Residue 601 [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]
PDB6nab Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with proline and adenosine monophophsphate (AMP)
Resolution2.0 Å
Binding residue
(original residue number in PDB)		E144 I152 R153 S154 F157 Q227 T230 G262 S264 R266
Binding residue
(residue number reindexed from 1)		E141 I149 R150 S151 F154 Q224 T227 G259 S261 R263
Annotation score5
Enzymatic activity
Enzyme Commision number 6.1.1.15: proline--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004827 proline-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006433 prolyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0017101 aminoacyl-tRNA synthetase multienzyme complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6nab, PDBe:6nab, PDBj:6nab
PDBsum6nab
PubMed
UniProtA0A4V8H034

[Back to BioLiP]