Structure of PDB 5yq7 Chain A Binding Site BS04

Receptor Information
>5yq7 Chain A (length=36) Species: 120962 (Roseiflexus castenholzii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PFEFRTSVVVSTLLGLVMALLIHFVVLSSGAFNWLR
Ligand information
Ligand IDKGD
InChIInChI=1S/C40H54O/c1-31(2)17-13-20-34(5)23-15-25-35(6)24-14-21-32(3)18-11-12-19-33(4)22-16-26-36(7)27-28-38-37(8)39(41)29-30-40(38,9)10/h11-12,14-19,21-28H,13,20,29-30H2,1-10H3/b12-11+,21-14+,22-16+,25-15+,28-27+,32-18+,33-19+,34-23+,35-24+,36-26+
InChIKeyBRKQDNOGSHYATK-HNNISBQLSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C1(C)(CCC(C(=C1C=[C@H]C(=[C@H]C=[C@H]C(=[C@H]C=[C@H]\C=C(/C)\C=[C@H]/C=C(/C=[C@H]/C=C(/CC\C=C(\C)C)C)C)C)C)C)=O)C
OpenEye OEToolkits 2.0.6CC1=C(C(CCC1=O)(C)C)/C=C/C(=C/C=C/C(=C/C=C/C=C(\C)/C=C/C=C(\C)/C=C/C=C(\C)/CCC=C(C)C)/C)/C
CACTVS 3.385CC(C)=CCC/C(C)=C/C=C/C(C)=C/C=C/C(C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)C(=O)CCC1(C)C
OpenEye OEToolkits 2.0.6CC1=C(C(CCC1=O)(C)C)C=CC(=CC=CC(=CC=CC=C(C)C=CC=C(C)C=CC=C(C)CCC=C(C)C)C)C
CACTVS 3.385CC(C)=CCCC(C)=CC=CC(C)=CC=CC(C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)CCC1(C)C
FormulaC40 H54 O
Namebeta,psi-caroten-4-one;
Keto-gamma-carotene
ChEMBL
DrugBank
ZINCZINC000059745718
PDB chain5yq7 Chain 9 Residue 101 [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]
PDB5yq7 Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote.
Resolution4.1 Å
Binding residue
(original residue number in PDB)		T16 L18 G19 M22 I26
Binding residue
(residue number reindexed from 1)		T12 L14 G15 M18 I22
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0042314 bacteriochlorophyll binding
GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
GO:0046872 metal ion binding
Biological Process
GO:0019684 photosynthesis, light reaction
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0019866 organelle inner membrane
GO:0030076 light-harvesting complex
GO:0030077 plasma membrane light-harvesting complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yq7, PDBe:5yq7, PDBj:5yq7
PDBsum5yq7
PubMed29674684
UniProtQ83XD1

[Back to BioLiP]