Structure of PDB 4ffr Chain A Binding Site BS02

Receptor Information
>4ffr Chain A (length=347) Species: 269797 (Methanosarcina barkeri str. Fusaro) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDV
IKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRI
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYDDKDE
PDTLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPAN
PLFRQISHDLAANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYY
SSGINLIELLFRAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMG
SDYGKFYEEPGIEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain4ffr Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ffr Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G8 K10 D31 K32 D49 V50 I51 N71 E72 N73 C76
Binding residue
(residue number reindexed from 1)		G8 K10 D31 K32 D49 V50 I51 N71 E72 N73 C76
Annotation score5
Enzymatic activity
Enzyme Commision number 6.3.2.59: 3-methyl-D-ornithine--L-lysine ligase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0008652 amino acid biosynthetic process
GO:0071524 pyrrolysine biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ffr, PDBe:4ffr, PDBj:4ffr
PDBsum4ffr
PubMed22985965
UniProtQ46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)

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