Structure of PDB 4zed Chain A Binding Site BS01

Receptor Information
>4zed Chain A (length=490) Species: 176299 (Agrobacterium fabrum str. C58) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RRALRLGVNGLPNSLEPVNAISNVGPRIVNQIFDTLIARDFFAKGAPGNA
IDLVPALAESWERIDEKSVRFKLRQKVMFHDGVELTADDVAYTFSSERLW
GPEAIKKIPLGKSYSLDFDEPVVEDKYTVTLRTKTPSYLIETFVASWMSR
IVPKEYYKKLGAVDFGNKPVGTGPYKFVEFVAGDRVVLEANDAYWGPKPT
ASKITYQIVAEPATRVAGLISGEYDIITTLTPDDIQLINSYPDLETRGTL
IENFHMFTFNMNQEVFKDKKLRRALALAVNRPIMVEALWKKQASIPAGFN
FPNYGETFDPKRKAMEYNVEEAKRLVKESGYDGTPITYHTMGNYYANAMP
ALMMMIEMWKQIGVNVVMKTYAPGSFPPDNQTWMRNWSNGQWMTDAYATI
VPEFGPNGQVQKRWGWKAPAEFNELCQKVTVLPNGKERFDAYNRMRDIFE
EEAPAVILYQPYDVYAARKDVHWKPVSFEMMEFRNNLSFG
Ligand information
Ligand IDAGW
InChIInChI=1S/C24H35O19P/c25-6-12-15(30)16(31)17(32)23(38-12)41-24(9-27)20(39-21(33)10-4-2-1-3-5-10)18(13(7-26)40-24)42-44(35,36)43-19-14(29)11(28)8-37-22(19)34/h1-5,11-20,22-23,25-32,34H,6-9H2,(H,35,36)/t11-,12+,13+,14-,15-,16+,17+,18+,19+,20-,22+,23+,24-/m0/s1
InChIKeyLMASXRQPXQBKBC-GJRQBPJOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)C(=O)OC2C(C(OC2(CO)OC3C(C(C(C(O3)CO)O)O)O)CO)OP(=O)(O)OC4C(C(COC4O)O)O
CACTVS 3.385OC[CH]1O[CH](O[C]2(CO)O[CH](CO)[CH](O[P](O)(=O)O[CH]3[CH](O)OC[CH](O)[CH]3O)[CH]2OC(=O)c4ccccc4)[CH](O)[CH](O)[CH]1O
CACTVS 3.385OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O[P](O)(=O)O[C@H]3[C@H](O)OC[C@H](O)[C@@H]3O)[C@@H]2OC(=O)c4ccccc4)[C@H](O)[C@H](O)[C@H]1O
OpenEye OEToolkits 1.7.6c1ccc(cc1)C(=O)O[C@H]2[C@@H]([C@H](O[C@@]2(CO)O[C@@H]3[C@@H]([C@@H]([C@H]([C@H](O3)CO)O)O)O)CO)OP(=O)(O)O[C@@H]4[C@H]([C@H](CO[C@H]4O)O)O
ACDLabs 12.01O=C(OC3C(OC1OC(CO)C(O)C(O)C1O)(OC(CO)C3OP(=O)(OC2C(O)C(O)COC2O)O)CO)c4ccccc4
FormulaC24 H35 O19 P
Name
ChEMBL
DrugBank
ZINCZINC000263620711
PDB chain4zed Chain A Residue 601 [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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PDB4zed A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		L42 N44 S53 N54 W178 M372 Y375 Y376 Y402 F407 W418 S419 N420 G421 E434 E510
Binding residue
(residue number reindexed from 1)		L11 N13 S22 N23 W147 M341 Y344 Y345 Y371 F376 W387 S388 N389 G390 E403 E479
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.12,Kd=7.5uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:1904680 peptide transmembrane transporter activity
Biological Process
GO:0015833 peptide transport
GO:0055085 transmembrane transport
Cellular Component
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space
GO:0043190 ATP-binding cassette (ABC) transporter complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4zed, PDBe:4zed, PDBj:4zed
PDBsum4zed
PubMed26244338
UniProtQ52012

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