Structure of PDB 6xm8 Chain A Binding Site BS02

Receptor Information
>6xm8 Chain A (length=483) Species: 627192 (Sphingobium sp. SYK-6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AHFPDTPAFTGFNAPSRIECDIPNLVHEGTIPPELNGAFFRVQPDPQFPP
RLGDDISFNGDGMITRFHIHDGQCDIKQRWAKTNKWKLENAAGKALFGSY
RNPLTDDESVKGEYRSTANTNAFVFAGKLWAMKEDSPSLTMDPATMETFG
FEKFGGKMTGQTFTAHPKVDPLTGNMVAIGYAASGLCTDDVCLYEISPDG
ELIYEAWFKVPYYCMMHDFGVTKDYLVLHIVPSIGSWDRLEKGLPHFGFD
TTLPVYLGIIPRRADLKQEDIRWFKRENCFASHVMNAFQEGTKVHVDVPE
AENNMFPFFPDVHGAPFNPQQAMSRLTRWTVDMASNSDEFDSVTRLTETA
GEFPRIDDRMTGLPYRYGWMLEMDMKRPVELGGFLMNCLFLKDHQTGAEQ
HWWCGPTSSLQEPAFIPRSKDAPEGDGWIVQVCNRLADHKSDLLIFEALD
IEKGPVATVHLPFALRFGLHGNWANAEEIGLAA
Ligand information
Ligand IDV5P
InChIInChI=1S/C16H16O4/c1-19-15-9-11(5-7-13(15)17)3-4-12-6-8-14(18)16(10-12)20-2/h3-10,17-18H,1-2H3/b4-3+
InChIKeyKQPXJFAYGYIGRU-ONEGZZNKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1cc(ccc1O)C=Cc2ccc(O)c(OC)c2
ACDLabs 12.01c1(ccc(O)c(c1)OC)\C=C\c2cc(c(cc2)O)OC
OpenEye OEToolkits 2.0.7COc1cc(ccc1O)/C=C/c2ccc(c(c2)OC)O
CACTVS 3.385COc1cc(ccc1O)\C=C\c2ccc(O)c(OC)c2
OpenEye OEToolkits 2.0.7COc1cc(ccc1O)C=Cc2ccc(c(c2)OC)O
FormulaC16 H16 O4
Namelignostilbene;
4,4'-[(E)-ethene-1,2-diyl]bis(2-methoxyphenol)
ChEMBLCHEMBL2260731
DrugBank
ZINCZINC000000185070
PDB chain6xm8 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6xm8 Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		F59 Y101 N120 T121 K134 M216 H218 H284 M306 E353 F354 L475
Binding residue
(residue number reindexed from 1)		F58 Y100 N119 T120 K133 M215 H217 H283 M305 E352 F353 L469
Annotation score1
Enzymatic activity
Enzyme Commision number 1.13.11.-
Gene Ontology
Molecular Function
GO:0010436 carotenoid dioxygenase activity
GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0016121 carotene catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6xm8, PDBe:6xm8, PDBj:6xm8
PDBsum6xm8
PubMed33965373
UniProtG2IQT9

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