Structure of PDB 4pp0 Chain A Binding Site BS01

Receptor Information
>4pp0 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
DGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPNTFLTTADSPL
LKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQM
MPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFG
PRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGY
DASP
Ligand information
Ligand IDOP1
InChIInChI=1S/C11H18N4O5/c12-11(13)14-5-1-2-6(9(17)18)15-7(10(19)20)3-4-8(15)16/h6-7H,1-5H2,(H,17,18)(H,19,20)(H4,12,13,14)/t6-,7+/m0/s1
InChIKeyGTRMYGUJZGMZEF-NKWVEPMBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=N)NCCC[CH](N1[CH](CCC1=O)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6C1CC(=O)N(C1C(=O)O)C(CCCNC(=N)N)C(=O)O
OpenEye OEToolkits 1.7.6[H]/N=C(\N)/NCCC[C@@H](C(=O)O)N1[C@H](CCC1=O)C(=O)O
ACDLabs 12.01O=C(O)C(N1C(=O)CCC1C(=O)O)CCCNC(=[N@H])N
CACTVS 3.385NC(=N)NCCC[C@H](N1[C@H](CCC1=O)C(O)=O)C(O)=O
FormulaC11 H18 N4 O5
Name1-[(1S)-4-carbamimidamido-1-carboxybutyl]-5-oxo-D-proline;
Pyronopaline
ChEMBL
DrugBank
ZINC
PDB chain4pp0 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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PDB4pp0 Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host.
Resolution1.57 Å
Binding residue
(original residue number in PDB)		E36 Y39 W77 A94 A95 G97 R102 Q165 T168 S169 H170 S207
Binding residue
(residue number reindexed from 1)		E9 Y12 W50 A67 A68 G70 R75 Q138 T141 S142 H143 S180
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.40,Kd=39.9uM
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4pp0, PDBe:4pp0, PDBj:4pp0
PDBsum4pp0
PubMed25299655
UniProtP35120|NOCT_AGRFC Nopaline-binding periplasmic protein (Gene Name=nocT)

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