Structure of PDB 8caw Chain A Binding Site BS01

Receptor Information
>8caw Chain A (length=491) Species: 358 (Agrobacterium tumefaciens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DRRALRIGVNGLPPSLEPINGISNTGPRIINQIFDALIRRDYFADGAKGN
NIKLVPALAESFERIDDKSIRFKLRQGVKFHNGAEMTAEDVAFTFSSERL
WGDEAIKTVPNGRNFSPNWDEPVVEDKYTVVLRTKTPSYLIEKYLGSWLG
PIVPKEYYKSLGAVAFGNKPIGTGPYKFRELVANDHVTLEANDGYWGDKP
TASTITYQVVAEPATRVAGLISGEYDIITTLTPDDMALVDGYSDLETRGT
LIENLHMFTFNMNQPIFQNKTLRRALALAVNRPLIVEALWKNKASIPNGF
NFPHYGATYDPKRKPMEFNLKEAKRLVKESGYDGTPITYHTMGNYYANAV
PALMMMIEMWKAAGITVVPKIFAPGTTPKDSDILIRNWSNGQWLTDGLTT
MVSEFGPGRGVQKRWGWKAPAEFNNLCDQVAQLKDGEERSAAFNRLRDIF
EDEAPAVLMYQPYDVYAARKDVQWSPVSFETMEFRGNLNFK
Ligand information
Ligand IDC84
InChIInChI=1S/C21H34N6O16P2/c1-7(2)12(30)15(33)19(34)26-45(38,39)42-10-3-8(29)20(41-10)27-6-24-11-17(22-5-23-18(11)27)25-44(36,37)43-16-14(32)13(31)9(4-28)40-21(16)35/h5-10,12-16,20-21,28-33,35H,3-4H2,1-2H3,(H2,26,34,38,39)(H2,22,23,25,36,37)/t8-,9+,10+,12-,13+,14-,15+,16+,20+,21+/m0/s1
InChIKeyKOMSNTWZRZGGEF-AIJJVVIGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)[CH](O)[CH](O)C(=O)N[P](O)(=O)O[CH]1C[CH](O)[CH](O1)n2cnc3c(N[P](O)(=O)O[CH]4[CH](O)O[CH](CO)[CH](O)[CH]4O)ncnc23
CACTVS 3.385CC(C)[C@H](O)[C@@H](O)C(=O)N[P](O)(=O)O[C@@H]1C[C@H](O)[C@@H](O1)n2cnc3c(N[P](O)(=O)O[C@H]4[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]4O)ncnc23
OpenEye OEToolkits 2.0.7CC(C)[C@@H]([C@H](C(=O)NP(=O)(O)O[C@@H]1C[C@@H]([C@@H](O1)n2cnc3c2ncnc3NP(=O)(O)O[C@@H]4[C@H]([C@@H]([C@H](O[C@H]4O)CO)O)O)O)O)O
OpenEye OEToolkits 2.0.7CC(C)C(C(C(=O)NP(=O)(O)OC1CC(C(O1)n2cnc3c2ncnc3NP(=O)(O)OC4C(C(C(OC4O)CO)O)O)O)O)O
FormulaC21 H34 N6 O16 P2
Name[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid;
Agrocin 84 (beta-D-glucopyranose form)
ChEMBL
DrugBank
ZINC
PDB chain8caw 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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PDB8caw A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity.
Resolution1.256 Å
Binding residue
(original residue number in PDB)
S53 N54 Y375 Y376 S419 N420 G421 E434 R444 E510
Binding residue
(residue number reindexed from 1)
S23 N24 Y345 Y346 S389 N390 G391 E404 R414 E480
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:8caw, PDBe:8caw, PDBj:8caw
PDBsum8caw
PubMed38058289
UniProtA5WYD2

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