Structure of PDB 8ckd Chain A Binding Site BS01

Receptor Information
>8ckd 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 IDY4H
InChIInChI=1S/C12H23O14P/c13-1-3-5(15)7(17)9(11(19)23-3)25-27(21,22)26-10-8(18)6(16)4(2-14)24-12(10)20/h3-20H,1-2H2,(H,21,22)/t3-,4-,5-,6-,7+,8+,9-,10-,11-,12+/m1/s1
InChIKeyDCDHSOINTWUWCZ-BTLHAWITSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC[C@H]1O[C@H](O)[C@H](O[P](O)(=O)O[C@H]2[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@@H](O)[C@@H]1O
CACTVS 3.385OC[CH]1O[CH](O)[CH](O[P](O)(=O)O[CH]2[CH](O)O[CH](CO)[CH](O)[CH]2O)[CH](O)[CH]1O
OpenEye OEToolkits 2.0.7C(C1C(C(C(C(O1)O)OP(=O)(O)OC2C(C(C(OC2O)CO)O)O)O)O)O
OpenEye OEToolkits 2.0.7C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)OP(=O)(O)O[C@@H]2[C@H]([C@@H]([C@H](O[C@@H]2O)CO)O)O)O)O)O
FormulaC12 H23 O14 P
NameAgrocinopine D-like (C2-C2 linked;
with an alpha and beta-D-glucopyranose);
Agrocinopine D-like;
[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate;
D-glucose-2-phosphate-2-glucose
ChEMBL
DrugBank
ZINC
PDB chain8ckd Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ckd A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity.
Resolution1.6 Å
Binding residue
(original residue number in PDB)
S53 N54 Y145 W178 Y375 Y376 W418 S419 N420 G421 T430 E434 E510
Binding residue
(residue number reindexed from 1)
S22 N23 Y114 W147 Y344 Y345 W387 S388 N389 G390 T399 E403 E479
Annotation score1
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

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Biological Process

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Cellular Component
External links
PDB RCSB:8ckd, PDBe:8ckd, PDBj:8ckd
PDBsum8ckd
PubMed38058289
UniProtQ52012

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