Structure of PDB 5yh8 Chain A Binding Site BS01

Receptor Information
>5yh8 Chain A (length=510) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PHMGLEEKKENKQLTYTTVKDIGDMNPHVYGGSMSAESMIYEPLVRNTKD
GIKPLLAKKWDVSEDGKTYTFHLRDDVKFHDGTPFDADAVKKNIDAVQEN
KKLHSWLKISTLIDNVKVKDKYTVELNLKEAYQPALAELAMPRPYVFVSP
KDFKNGTTKDGVKKFDGTGPFKLGEHKKDESADFNKNDQYWGEKSKLNKV
QAKVMPAGETAFLSMKKGETNFAFTDDRGTDSLDKDSLKQLKDTGDYQVK
RSQPMNTKMLVVNSGKKDNAVSDKTVRQAIGHMVNRDKIAKEILDGQEKP
ATQLFAKNVTDINFDMPTRKYDLKKAESLLDEAGWKKGKDSDVRQKDGKN
LEMAMYYDKGSSSQKEQAEYLQAEFKKMGIKLNINGETSDKIAERRTSGD
YDLMFNQTWGLLYDPQSTIAAFKAKNGYESATSGIENKDKIYNSIDDAFK
IQNGKERSDAYKNILKQIDDEGIFIPISHGSMTVVAPKDLEKVSFTQSQY
ELPFNEMQYK
Ligand information
Ligand ID8UX
InChIInChI=1S/C13H20N4O6/c1-7(11(18)19)17-9(12(20)21)2-3-15-10(13(22)23)4-8-5-14-6-16-8/h5-7,9-10,15,17H,2-4H2,1H3,(H,14,16)(H,18,19)(H,20,21)(H,22,23)/t7-,9-,10+/m0/s1
InChIKeyWLNNYKMTYVPSDL-UJNFCWOMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C(=O)O)NC(CCNC(Cc1c[nH]cn1)C(=O)O)C(=O)O
CACTVS 3.385C[CH](N[CH](CCN[CH](Cc1c[nH]cn1)C(O)=O)C(O)=O)C(O)=O
CACTVS 3.385C[C@H](N[C@@H](CCN[C@H](Cc1c[nH]cn1)C(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 2.0.6C[C@@H](C(=O)O)N[C@@H](CCN[C@H](Cc1c[nH]cn1)C(=O)O)C(=O)O
FormulaC13 H20 N4 O6
Name(2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid;
staphylopine
ChEMBL
DrugBank
ZINC
PDB chain5yh8 Chain A Residue 602 [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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PDB5yh8 Mechanistic insights into staphylopine-mediated metal acquisition
Resolution2.12 Å
Binding residue
(original residue number in PDB)		Y27 W103 R140 D224 R225 R393 W406 Y410 N423 Y497
Binding residue
(residue number reindexed from 1)		Y30 W106 R143 D227 R228 R396 W409 Y413 N426 Y500
Annotation score1
Binding affinityMOAD: Kd=167.8nM
PDBbind-CN: -logKd/Ki=6.78,Kd=167.8nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016151 nickel cation binding
GO:0020037 heme binding
GO:1904680 peptide transmembrane transporter activity
Biological Process
GO:0006824 cobalt ion transport
GO:0006829 zinc ion transport
GO:0015675 nickel cation transport
GO:0015833 peptide transport
GO:0055085 transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space
GO:0043190 ATP-binding cassette (ABC) transporter complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yh8, PDBe:5yh8, PDBj:5yh8
PDBsum5yh8
PubMed29581261
UniProtQ2FVE7|CNTA_STAA8 Metal-staphylopine-binding protein CntA (Gene Name=cntA)

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