Structure of PDB 5nc5 Chain B Binding Site BS01

Receptor Information

>5nc5 Chain B (length=1033) Species: 83333 (Escherichia coli K-12)

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYP
GADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDA
DIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMT
QEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTP
VDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKIL
LKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANAL
DTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIIL
VFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVL
AIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLS
AVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPI
AKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVV
GMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLT
KEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMR
ATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARN
QLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTL
GAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVP
FSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASK
LPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFS
VMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAK
DLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQ
NAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRF

Ligand information

• Ligand ID: PUY
• InChI: InChI=1S/C22H29N7O5/c1-28(2)19-17-20(25-10-24-19)29(11-26-17)22-18(31)16(15(9-30)34-22)27-21(32)14(23)8-12-4-6-13(33-3)7-5-12/h4-7,10-11,14-16,18,22,30-31H,8-9,23H2,1-3H3,(H,27,32)/t14-,15+,16+,18+,22+/m0/s1
• InChIKey: RXWNCPJZOCPEPQ-NVWDDTSBSA-N
• SMILES:
  ACDLabs 10.04: O=C(NC3C(OC(n2cnc1c2ncnc1N(C)C)C3O)CO)C(N)Cc4ccc(OC)cc4
  CACTVS 3.341: COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO)n3cnc4c(ncnc34)N(C)C)cc1
  OpenEye OEToolkits 1.5.0: CN(C)c1c2c(ncn1)n(cn2)C3C(C(C(O3)CO)NC(=O)C(Cc4ccc(cc4)OC)N)O
  OpenEye OEToolkits 1.5.0: CN(C)c1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)NC(=O)[C@H](Cc4ccc(cc4)OC)N)O
  CACTVS 3.341: COc1ccc(C[CH](N)C(=O)N[CH]2[CH](O)[CH](O[CH]2CO)n3cnc4c(ncnc34)N(C)C)cc1
• Formula: C22 H29 N7 O5
• Name: PUROMYCIN
• ChEMBL: CHEMBL469912
• DrugBank: DB08437
• ZINC: ZINC000053147179
• PDB chain: 5nc5 Chain B Residue 1120

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5nc5 An allosteric transport mechanism for the AcrAB-TolC Multidrug Efflux Pump.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): S134 F136 F178 M573 F617 F666 L668 V672
• Binding residue (residue number reindexed from 1): S134 F136 F178 M573 F617 F666 L668 V672
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0015125 bile acid transmembrane transporter activity
• GO:0015562 efflux transmembrane transporter activity
• GO:0015567 alkane transmembrane transporter activity
• GO:0022857 transmembrane transporter activity
• GO:0042802 identical protein binding
• GO:0042910 xenobiotic transmembrane transporter activity
• GO:0042931 enterobactin transmembrane transporter activity

Biological Process

• GO:0009410 response to xenobiotic stimulus
• GO:0009636 response to toxic substance
• GO:0015721 bile acid and bile salt transport
• GO:0015895 alkane transport
• GO:0015908 fatty acid transport
• GO:0042908 xenobiotic transport
• GO:0042930 enterobactin transport
• GO:0046677 response to antibiotic
• GO:0055085 transmembrane transport
• GO:0140330 xenobiotic detoxification by transmembrane export across the cell outer membrane

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0098567 periplasmic side of plasma membrane
• GO:1990281 efflux pump complex

External links

• PDB: RCSB:5nc5, PDBe:5nc5, PDBj:5nc5
• PDBsum: 5nc5
• PubMed: 28355133
• UniProt: P31224|ACRB_ECOLI Multidrug efflux pump subunit AcrB (Gene Name=acrB)