Structure of PDB 4qnu Chain A Binding Site BS01

Receptor Information
>4qnu Chain A (length=323) Species: 405955 (Escherichia coli APEC O1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIDFGNFYSLIAKNHLSHWLETLPAQIANWQREQQHGLFKQWSNAVEFLP
EIKPYRLDLLHSVTAESEEPLSAGQIKRIETLMRNLMPWRKGPFSLYGVN
IDTEWRSDWKWDRVLPHLSDLTGRTILDVGCGSGYHMWRMIGAGAHLAVG
IDPTQLFLCQFEAVRKLLGNDQRAHLLPLGIEQLPALKAFDTVFSMGVLY
HRRSPLEHLWQLKDQLVNEGELVLETLVIDGDENTVLVPGDRYAQMRNVY
FIPSALALKNWLKKCGFVDIRIADVSVTTTEEQRRTEWMVTESLADFLDP
HDPGKTVEGYPAPKRAVLIARKP
Ligand information
Ligand IDGEK
InChIInChI=1S/C16H22N6O7S/c17-7(16(27)28)1-2-30(4-9(23)24)3-8-11(25)12(26)15(29-8)22-6-21-10-13(18)19-5-20-14(10)22/h5-8,11-12,15,25-26H,1-4,17H2,(H3-,18,19,20,23,24,27,28)/t7-,8+,11+,12+,15+,30-/m0/s1
InChIKeyVFFTYSZNZJBRBG-HEOPWLPUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](C[S+](CC[CH]([NH3+])C([O-])=O)CC([O-])=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[S@+](CC[C@@H](C(=O)[O-])[NH3+])CC(=O)[O-])O)O)N
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)C[S+](CCC(C(=O)[O-])[NH3+])CC(=O)[O-])O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](C[S@+](CC[C@H]([NH3+])C([O-])=O)CC([O-])=O)[C@@H](O)[C@H]3O
ACDLabs 12.01[O-]C(=O)C[S+](CCC(C([O-])=O)[NH3+])CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC16 H22 N6 O7 S
Name(2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate;
CARBOXY-S-ADENOSYLMETHIONINE
ChEMBL
DrugBank
ZINC
PDB chain4qnu Chain A Residue 401 [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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PDB4qnu Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification.
Resolution2.6 Å
Binding residue
(original residue number in PDB)
K91 K110 G130 D152 P153 F157 I181 M196 G197 Y200 R315
Binding residue
(residue number reindexed from 1)
K91 K110 G130 D152 P153 F157 I181 M196 G197 Y200 R315
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=6.40,Kd=0.40uM
Enzymatic activity
Enzyme Commision number 2.5.1.-
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
Biological Process
GO:0002098 tRNA wobble uridine modification
GO:0006400 tRNA modification
GO:0008033 tRNA processing

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:4qnu, PDBe:4qnu, PDBj:4qnu
PDBsum4qnu
PubMed25855808
UniProtA1AC32|CMOB_ECOK1 tRNA U34 carboxymethyltransferase (Gene Name=cmoB)

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