Structure of PDB 3dp8 Chain A Binding Site BS01

Receptor Information
>3dp8 Chain A (length=498) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLA
KSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWL
ELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHE
TMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPD
PTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVML
ALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYA
NLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDA
LSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAP
YDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALY
RDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP
Ligand information
Ligand IDHCT
InChIInChI=1S/C7H10O6/c8-5(9)2-1-4(7(12)13)3-6(10)11/h4H,1-3H2,(H,8,9)(H,10,11)(H,12,13)/t4-/m1/s1
InChIKeyLOGBRYZYTBQBTB-SCSAIBSYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)CC[C@H](CC(O)=O)C(O)=O
OpenEye OEToolkits 1.5.0C(CC(=O)O)[C@H](CC(=O)O)C(=O)O
CACTVS 3.341OC(=O)CC[CH](CC(O)=O)C(O)=O
OpenEye OEToolkits 1.5.0C(CC(=O)O)C(CC(=O)O)C(=O)O
ACDLabs 10.04O=C(O)CCC(C(=O)O)CC(=O)O
FormulaC7 H10 O6
Name(2R)-butane-1,2,4-tricarboxylic acid
ChEMBL
DrugBank
ZINCZINC000001586744
PDB chain3dp8 Chain A Residue 511 [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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PDB3dp8 Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y22 W100 R137 W398 H416
Binding residue
(residue number reindexed from 1)		Y21 W99 R136 W397 H415
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0016151 nickel cation binding
GO:0020037 heme binding
GO:0046914 transition metal ion binding
GO:0051540 metal cluster binding
GO:1904680 peptide transmembrane transporter activity
Biological Process
GO:0015675 nickel cation transport
GO:0015833 peptide transport
GO:0050919 negative chemotaxis
GO:0055085 transmembrane transport
GO:0098716 nickel cation import across plasma membrane
Cellular Component
GO:0016020 membrane
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space
GO:0043190 ATP-binding cassette (ABC) transporter complex
GO:0055052 ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dp8, PDBe:3dp8, PDBj:3dp8
PDBsum3dp8
PubMed18759453
UniProtP33590|NIKA_ECOLI Nickel-binding periplasmic protein (Gene Name=nikA)

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