1GZM

Structure of Bovine Rhodopsin in a Trigonal Crystal Form

PDB DOI: https://doi.org/10.2210/pdb1GZM/pdb

Classification: SIGNALING PROTEIN
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2002-05-24 Released: 2003-11-20
Deposition Author(s): Li, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.235
R-Value Work: 0.202
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 3C9L

Macromolecule Content

Total Structure Weight: 87.94 kDa
Atom Count: 5,792
Modelled Residue Count: 660
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): 0 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, D, E, F	3		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEF Query on PEF Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain X [auth B] MOL2 format, chain J [auth A] MOL2 format, chain X [auth B]	J [auth A], X [auth B]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C₃₇ H₇₄ N O₈ P SLKDGVPOSSLUAI-PGUFJCEWSA-N		Interactions Focus chain J [auth A] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain X [auth B]
C8E Query on C8E Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] L [auth A] M [auth A] AA [auth B], BA [auth B], CA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], V [auth B], W [auth B], Z [auth B]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth B]
RET Query on RET Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain S [auth B]	G [auth A], S [auth B]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain G [auth A] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain S [auth B]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	H [auth A], I [auth A], T [auth B], U [auth B]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain T [auth B] Focus chain U [auth B]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain K [auth A] SDF format, chain Y [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Y [auth B]	DA [auth B], K [auth A], Y [auth B]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain K [auth A] Focus chain Y [auth B] Interactions & Density Focus chain DA [auth B] Focus chain K [auth A] Focus chain Y [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain EA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain EA [auth B]	EA [auth B], R [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain R [auth A] Interactions & Density Focus chain EA [auth B] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.235
R-Value Work: 0.202
R-Value Observed: 0.202
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.82	α = 90
b = 103.82	β = 90
c = 76.59	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-11-20

Deposition Author(s):

Li, J.

Revision History (Full details and data files)

Version 1.0: 2003-11-20
Type: Initial release
Version 1.1: 2011-10-19
Changes: Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
Version 1.2: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary