Structure of PDB 3o9p Chain A Binding Site BS01

Receptor Information
>3o9p Chain A (length=509) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TVLAEKQELVRHIKDEPASLDPAKAVGLPEIQVIRDLFEGLVNQNEKGEI
VPGVATQWKSNDNRIWTFTLRDNAKWADGTPVTAQDFVYSWQRLVDPKTL
SPFAWFAALAGINNAQAIIDGKATPDQLGVTAVDAHTLKIQLDKPLPWFV
NLTANFAFFPVQKANVESGKEWTKPGNLIGNGAYVLKERVVNEKLVVVPN
THYWDNAKTVLQKVTFLPINQESAATKRYLAGDIDITESFPKNMYQKLLK
DIPGQVYTPPQLGTYYYAFNTQKGPTADQRVRLALSMTIDRRLMTEKVLG
TGEKPAWHFTPDVTAGFTPEPSPFEQMSQEELNAQAKTLLSAAGYGPQKP
LKLTLLYNTSENHQKIAIAVASMWKKNLGVDVKLQNQEWKTYIDSRNTGN
FDVIRASWVGDYNEPSTFLTLLTSTHSGNISRFNNPAYDKVLAQASTENT
VKARNADYNAAEKILMEQAPIAPIYQYTNGRLIKPWLKGYPINNPEDVAY
SRTMYIVKH
Ligand information
Ligand IDMHI
InChIInChI=1S/C15H26N4O8/c1-7(16)12(21)19-10(15(26)27)5-6-11(20)18-9(14(24)25)4-2-3-8(17)13(22)23/h7-10H,2-6,16-17H2,1H3,(H,18,20)(H,19,21)(H,22,23)(H,24,25)(H,26,27)/t7-,8+,9-,10+/m0/s1
InChIKeyFMNCPUGORYYCEM-QCLAVDOMSA-N
SMILES
SoftwareSMILES
CACTVS 3.352C[CH](N)C(=O)N[CH](CCC(=O)N[CH](CCC[CH](N)C(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 1.6.1CC(C(=O)NC(CCC(=O)NC(CCCC(C(=O)O)N)C(=O)O)C(=O)O)N
CACTVS 3.352C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 1.6.1C[C@@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=O)O)N)C(=O)O)C(=O)O)N
FormulaC15 H26 N4 O8
NameL-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID
ChEMBLCHEMBL1738838
DrugBank
ZINCZINC000031259714
PDB chain3o9p Chain A Residue 516 [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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PDB3o9p Compensating Stereochemical Changes Allow Murein Tripeptide to Be Accommodated in a Conventional Peptide-binding Protein.
Resolution2.07 Å
Binding residue
(original residue number in PDB)		K20 V32 L34 Q267 R402 R411 S413 W414 V415 D417 Y483 T484
Binding residue
(residue number reindexed from 1)		K14 V26 L28 Q261 R396 R405 S407 W408 V409 D411 Y477 T478
Annotation score1
Binding affinityMOAD: Kd=0.3uM
PDBbind-CN: -logKd/Ki=6.52,Kd=0.3uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:1900750 oligopeptide binding
GO:1904680 peptide transmembrane transporter activity
Biological Process
GO:0015031 protein transport
GO:0015833 peptide transport
GO:0015834 peptidoglycan-associated peptide transport
GO:0035351 heme transmembrane transport
GO:0042938 dipeptide transport
GO:0042939 tripeptide transport
GO:0055085 transmembrane transport
GO:0140207 tripeptide 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:3o9p, PDBe:3o9p, PDBj:3o9p
PDBsum3o9p
PubMed21705338
UniProtP77348|MPPA_ECOLI Periplasmic murein peptide-binding protein MppA (Gene Name=mppA)

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