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BioLiP

Structure of PDB 5ota Chain A Binding Site BS01

Receptor Information
>5ota Chain A (length=254) Species: 176299 (Agrobacterium fabrum str. C58) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAW
DGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPMTFLTTADSPL
LKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQM
MPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFG
PRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGY
DASP
Ligand information
Ligand IDAQQ
InChIInChI=1S/C8H16N2O4/c1-5(7(11)12)10-6(8(13)14)3-2-4-9/h5-6,10H,2-4,9H2,1H3,(H,11,12)(H,13,14)/t5-,6+/m1/s1
InChIKeyZQKXJZFWRBQTIO-RITPCOANSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@H](C(=O)O)N[C@@H](CCCN)C(=O)O
OpenEye OEToolkits 2.0.6CC(C(=O)O)NC(CCCN)C(=O)O
CACTVS 3.385C[CH](N[CH](CCCN)C(O)=O)C(O)=O
CACTVS 3.385C[C@@H](N[C@@H](CCCN)C(O)=O)C(O)=O
FormulaC8 H16 N2 O4
Name(2~{S})-5-azanyl-2-[[(2~{R})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]pentanoic acid
ChEMBL
DrugBank
ZINCZINC000002522560
PDB chain5ota Chain A Residue 301 [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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PDB5ota Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E36 Y39 W77 A95 G97 R102 M117 Q165 T168 S169 H170 S207
Binding residue
(residue number reindexed from 1)		E9 Y12 W50 A68 G70 R75 M90 Q138 T141 S142 H143 S180
Annotation score1
Binding affinityMOAD: Kd=4.4uM
PDBbind-CN: -logKd/Ki=5.74,Kd=1.8uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0015276 ligand-gated monoatomic ion channel activity
Biological Process
GO:0034220 monoatomic ion transmembrane transport
GO:0071705 nitrogen compound transport
Cellular Component
GO:0016020 membrane
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ota, PDBe:5ota, PDBj:5ota
PDBsum5ota
PubMed29269740
UniProtP35120|NOCT_AGRFC Nopaline-binding periplasmic protein (Gene Name=nocT)

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