Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin
Taguchi, S., Niwa, S., Dao, H.A., Tanaka, Y., Takeda, R., Fukai, S., Hasegawa, K., Takeda, K.(2023) Commun Biol 6: 190
Experimental Data Snapshot
Starting Model: experimental
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(2023) Commun Biol 6: 190
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Bacteriorhodopsin | 230 | Halobacterium salinarum NRC-1 | Mutation(s): 0 Membrane Entity: Yes | ||
UniProt | |||||
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore P02945 Go to UniProtKB: P02945 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02945 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 3 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
L2P Query on L2P | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | 2,3-DI-PHYTANYL-GLYCEROL C43 H88 O3 ISDBCJSGCHUHFI-UMZPFTBHSA-N | |||
SQU Query on SQU | H [auth A], R [auth A], S [auth A], T [auth A] | 2,10,23-TRIMETHYL-TETRACOSANE C27 H56 ZADHKSJXSZBQFB-HHHXNRCGSA-N | |||
RET Query on RET | B [auth A] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 60.57 | α = 90 |
b = 60.57 | β = 90 |
c = 110.89 | γ = 120 |
Software Name | Purpose |
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SHELX | refinement |
XDS | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
CNS | phasing |
Funding Organization | Location | Grant Number |
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Japan Society for the Promotion of Science (JSPS) | Japan | -- |