Structure of PDB 1f88 Chain A Binding Site BS02

Receptor Information

>1f88 Chain A (length=338) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIML
GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
GYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE
NHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNN
ESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAASATTQKAEKEVTRMV
IIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPV
IYIMMNKQFRNCMVTTLCCGKNPSTTVSKTETSQVAPA

Ligand information

Ligand ID

RET

InChI

InChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6+,12-11+,16-8+,17-13+

InChIKey

NCYCYZXNIZJOKI-OVSJKPMPSA-N

SMILES

Software	SMILES
CACTVS 3.370	CC(=C\C=O)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C
ACDLabs 12.01	O=C\C=C(\C=C\C=C(\C=C\C1=C(C)CCCC1(C)C)C)C
OpenEye OEToolkits 1.7.0	CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C=O)/C)/C
OpenEye OEToolkits 1.7.0	CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC=O)C)C
CACTVS 3.370	CC(=CC=O)C=CC=C(C)C=CC1=C(C)CCCC1(C)C

Formula

C20 H28 O

Name

RETINAL

PDB chain

1f88 Chain A Residue 977 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	1f88 Crystal structure of rhodopsin: A G protein-coupled receptor.
Resolution	2.8 Å
Binding residue (original residue number in PDB)	A117 T118 G121 E122 S186 C187 M207 F212 W265 Y268 A269 K296
Binding residue (residue number reindexed from 1)	A117 T118 G121 E122 S186 C187 M207 F212 W261 Y264 A265 K292
Annotation score	4

Enzymatic activity

Enzyme Commision number

Gene Ontology

	Molecular Function
GO:0001965	G-protein alpha-subunit binding
GO:0002046	opsin binding
GO:0004930	G protein-coupled receptor activity
GO:0005085	guanyl-nucleotide exchange factor activity
GO:0005502	11-cis retinal binding
GO:0005515	protein binding
GO:0008020	G protein-coupled photoreceptor activity
GO:0008270	zinc ion binding
GO:0009881	photoreceptor activity
GO:0042802	identical protein binding
GO:0046872	metal ion binding
GO:1990763	arrestin family protein binding

	Biological Process
GO:0000226	microtubule cytoskeleton organization
GO:0007186	G protein-coupled receptor signaling pathway
GO:0007601	visual perception
GO:0007602	phototransduction
GO:0007603	phototransduction, visible light
GO:0009416	response to light stimulus
GO:0009583	detection of light stimulus
GO:0009642	response to light intensity
GO:0010467	gene expression
GO:0016038	absorption of visible light
GO:0016056	G protein-coupled opsin signaling pathway
GO:0043052	thermotaxis
GO:0045494	photoreceptor cell maintenance
GO:0050953	sensory perception of light stimulus
GO:0050960	detection of temperature stimulus involved in thermoception
GO:0060041	retina development in camera-type eye
GO:0071482	cellular response to light stimulus
GO:0071800	podosome assembly
GO:1904389	rod bipolar cell differentiation

	Cellular Component
GO:0000139	Golgi membrane
GO:0001750	photoreceptor outer segment
GO:0001917	photoreceptor inner segment
GO:0005794	Golgi apparatus
GO:0005886	plasma membrane
GO:0005911	cell-cell junction
GO:0016020	membrane
GO:0019867	outer membrane
GO:0042622	photoreceptor outer segment membrane
GO:0042995	cell projection
GO:0060342	photoreceptor inner segment membrane
GO:0097225	sperm midpiece
GO:0097381	photoreceptor disc membrane
GO:0097648	G protein-coupled receptor complex
GO:0120200	rod photoreceptor outer segment
GO:1990913	sperm head plasma membrane

View graph for
Molecular Function

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Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:1f88, PDBe:1f88, PDBj:1f88
PDBsum	1f88
PubMed	10926528
UniProt	P02699\|OPSD_BOVIN Rhodopsin (Gene Name=RHO)

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