3OAX

Crystal structure of bovine rhodopsin with beta-ionone

PDB DOI: https://doi.org/10.2210/pdb3OAX/pdb

Classification: SIGNALING PROTEIN
Organism(s): Bos taurus
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2010-08-05 Released: 2011-01-19
Deposition Author(s): Makino, C.L., Riley, C.K., Looney, J., Crouch, R.K., Okada, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.262
R-Value Work: 0.224
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 85.71 kDa
Atom Count: 6,015
Modelled Residue Count: 698
Deposited Residue Count: 698
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A, B	349	Bos taurus	Mutation(s): 1 Membrane Entity: Yes
UniProt
Find proteins for P02699 (Bos taurus) Explore P02699 Go to UniProtKB: P02699
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02699
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	2		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HTG Query on HTG Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain R [auth A] SDF format, chain FA [auth B] SDF format, chain S [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain S [auth A]	FA [auth B], GA [auth B], R [auth A], S [auth A]	heptyl 1-thio-beta-D-glucopyranoside C₁₃ H₂₆ O₅ S HPEGNLMTTNTJSP-LBELIVKGSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain R [auth A] Focus chain S [auth A]
RET Query on RET Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain U [auth B] MOL2 format, chain G [auth A] MOL2 format, chain U [auth B]	G [auth A], U [auth B]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain G [auth A] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain U [auth B]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain V [auth B] SDF format, chain H [auth A] SDF format, chain W [auth B] MOL2 format, chain I [auth A] MOL2 format, chain V [auth B] MOL2 format, chain H [auth A] MOL2 format, chain W [auth B]	H [auth A], I [auth A], V [auth B], W [auth B]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain V [auth B] Focus chain W [auth B]
4E6 Query on 4E6 Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain Q [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain Q [auth A]	EA [auth B], Q [auth A]	(4E,6E)-hexadeca-1,4,6-triene C₁₆ H₂₈ OPBISVRDVDRVHM-PTSVWTKZSA-N		Interactions Focus chain EA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain EA [auth B] Focus chain Q [auth A]
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Y [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain X [auth B] SDF format, chain Z [auth B] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B]	J [auth A] K [auth A] L [auth A] X [auth B] Y [auth B] J [auth A], K [auth A], L [auth A], X [auth B], Y [auth B], Z [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ID3 Query on ID3 Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain T [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain T [auth A]	HA [auth B], T [auth A]	(3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one C₁₃ H₂₀ O PSQYTAPXSHCGMF-BQYQJAHWSA-N		Interactions Focus chain HA [auth B] Focus chain T [auth A] Interactions & Density Focus chain HA [auth B] Focus chain T [auth A]
HTO Query on HTO Download Ideal Coordinates CCD File SDF format, chain DA [auth B] MOL2 format, chain DA [auth B]	DA [auth B]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain DA [auth B] Interactions & Density Focus chain DA [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A]	AA [auth B] BA [auth B] CA [auth B] M [auth A] N [auth A] AA [auth B], BA [auth B], CA [auth B], M [auth A], N [auth A], O [auth A], P [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.262
R-Value Work: 0.224
R-Value Observed: 0.224
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.99	α = 90
b = 96.99	β = 90
c = 149.8	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-01-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary