Structure of PDB 4i9d Chain A Binding Site BS01

Receptor Information
>4i9d Chain A (length=498) Species: 469008 (Escherichia coli BL21(DE3)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAK
SWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLE
LANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHET
MNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDP
TTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLA
LNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYAN
LGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDAL
SKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPY
DPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYR
DILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPV
Ligand information
Ligand IDL4D
InChIInChI=1S/C17H22N4O2.Fe/c1-20(12-15-6-2-4-8-18-15)10-11-21(14-17(22)23)13-16-7-3-5-9-19-16;/h2-9H,10-14H2,1H3,(H,22,23);/q;+3/p-1
InChIKeyKEGLXUIHTNIIAB-UHFFFAOYSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C[N]12CC[N]34[Fe+2]1([N]5=C(C2)C=CC=C5)([N]6=CC=CC=C6C3)OC(=O)C4
CACTVS 3.370CN12|[Fe++]|3|4(OC(=O)CN|3(CC1)Cc5ccccn|45)|n6ccccc6C2
ACDLabs 12.01O=C5O[Fe+2]346n1ccccc1CN6(CCN4(Cc2ccccn23)C)C5
FormulaC17 H21 Fe N4 O2
Name{(S)-N-(2-{methyl[(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)-N-[(pyridin-2-yl-kappaN)methyl]glycinato-kappa~2~N,O}iron(2+);
{N,N'-Bis(2-pyridylmethyl)-N-carboxymethyl-N'-methyl}iron(2+)
ChEMBL
DrugBank
ZINC
PDB chain4i9d Chain A Residue 631 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4i9d An artificial oxygenase built from scratch: substrate binding site identified using a docking approach.
Resolution1.7 Å
Binding residue
(original residue number in PDB)
Y22 T23 M27 W100 R137 W398 Y402 T490
Binding residue
(residue number reindexed from 1)
Y20 T21 M25 W98 R135 W396 Y400 T488
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.3.24: Transferred entry: 7.2.2.11.
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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Cellular Component
External links
PDB RCSB:4i9d, PDBe:4i9d, PDBj:4i9d
PDBsum4i9d
PubMed23440925
UniProtP33590|NIKA_ECOLI Nickel-binding periplasmic protein (Gene Name=nikA)

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