Structure of PDB 3od2 Chain A Binding Site BS03

Receptor Information
>3od2 Chain A (length=132) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGT
QGFAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAV
LKGDMGDVQHFADDVIAQRGVRHGHLQCLPKE
Ligand information
Ligand ID3CM
InChIInChI=1S/C21H38O11/c22-9-12-14(24)15(25)17(27)21(30-12)32-19-13(10-23)31-20(18(28)16(19)26)29-8-4-7-11-5-2-1-3-6-11/h11-28H,1-10H2/t12-,13-,14-,15+,16-,17-,18-,19-,20-,21-/m1/s1
InChIKeyFDBLAHXBTQUZSM-ZESVGKPKSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O(CCCC1CCCCC1)C3OC(C(OC2OC(CO)C(O)C(O)C2O)C(O)C3O)CO
OpenEye OEToolkits 1.7.0C1CCC(CC1)CCCOC2C(C(C(C(O2)CO)OC3C(C(C(C(O3)CO)O)O)O)O)O
OpenEye OEToolkits 1.7.0C1CCC(CC1)CCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
CACTVS 3.370OC[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](OCCCC3CCCCC3)O[CH]2CO)[CH](O)[CH](O)[CH]1O
CACTVS 3.370OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](OCCCC3CCCCC3)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1O
FormulaC21 H38 O11
Name3-CYCLOHEXYLPROPYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE;
CYMAL-3
ChEMBL
DrugBank
ZINCZINC000058638358
PDB chain3od2 Chain B Residue 134 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3od2 Structural basis of low-affinity nickel binding to the nickel-responsive transcription factor NikR from Escherichia coli.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		L19 S20 R23 Y25
Binding residue
(residue number reindexed from 1)		L19 S20 R23 Y25
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000976 transcription cis-regulatory region binding
GO:0001046 core promoter sequence-specific DNA binding
GO:0001217 DNA-binding transcription repressor activity
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
GO:0005515 protein binding
GO:0016151 nickel cation binding
GO:0042802 identical protein binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0010045 response to nickel cation
GO:2000143 negative regulation of DNA-templated transcription initiation
Cellular Component
GO:0005667 transcription regulator complex
GO:0032993 protein-DNA complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3od2, PDBe:3od2, PDBj:3od2
PDBsum3od2
PubMed20704276
UniProtP0A6Z6|NIKR_ECOLI Nickel-responsive regulator (Gene Name=nikR)

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