Structure of PDB 4ra1 Chain A Binding Site BS01

Receptor Information
>4ra1 Chain A (length=490) Species: 358 (Agrobacterium tumefaciens) [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 IDALX
InChIInChI=1S/C6H13O9P/c7-1-2-3(8)4(9)5(6(10)14-2)15-16(11,12)13/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5-,6+/m1/s1
InChIKeySIUIENVKPUKAHD-DVKNGEFBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC[C@H]1O[C@H](O)[C@H](O[P](O)(O)=O)[C@@H](O)[C@@H]1O
ACDLabs 12.01O=P(OC1C(O)C(O)C(OC1O)CO)(O)O
OpenEye OEToolkits 1.7.6C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)OP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6C(C1C(C(C(C(O1)O)OP(=O)(O)O)O)O)O
CACTVS 3.385OC[CH]1O[CH](O)[CH](O[P](O)(O)=O)[CH](O)[CH]1O
FormulaC6 H13 O9 P
Name2-O-phosphono-alpha-D-glucopyranose;
2-O-phosphono-alpha-D-glucose;
2-O-phosphono-D-glucose;
2-O-phosphono-glucose
ChEMBL
DrugBank
ZINCZINC000197875193
PDB chain4ra1 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4ra1 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)		S53 N54 Y145 W178 Y375 Y376 W418 S419 N420 T430 E434 E510
Binding residue
(residue number reindexed from 1)		S22 N23 Y114 W147 Y344 Y345 W387 S388 N389 T399 E403 E479
Annotation score1
Binding affinityMOAD: Kd=0.43uM
PDBbind-CN: -logKd/Ki=5.94,Kd=1.16uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ra1, PDBe:4ra1, PDBj:4ra1
PDBsum4ra1
PubMed26244338
UniProtQ52012

[Back to BioLiP]