2G87 | pdb_00002g87

Crystallographic model of bathorhodopsin

PDB DOI: https://doi.org/10.2210/pdb2G87/pdb

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

Deposited: 2006-03-02 Released: 2006-09-02
Deposition Author(s): Nakamichi, H., Okada, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.181 (Depositor)
R-Value Work:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystallographic analysis of primary visual photochemistry

Nakamichi, H., Okada, T.

(2006) Angew Chem Int Ed Engl 45: 4270-4273

PubMed: 16586416 Search on PubMed
DOI: https://doi.org/10.1002/anie.200600595
Primary Citation Related Structures:
2G87

Organizational Affiliation

Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.

Macromolecule Content

Total Structure Weight: 85.39 kDa
Atom Count: 5,948
Modeled Residue Count: 698
Deposited Residue Count: 698
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02699
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-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
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-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
Glycosylation Resources
GlyTouCan: G31886NL GlyCosmos: G31886NL GlyGen: G31886NL

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.181 (Depositor)
R-Value Work: 0.178 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.49	α = 90
b = 96.49	β = 90
c = 150.4	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-09-02

Deposition Author(s):

Nakamichi, H.

Okada, T.

Revision History (Full details and data files)

Version 1.0: 2006-09-02
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

2G87 | pdb_00002g87

Crystallographic model of bathorhodopsin

Literature

Crystallographic analysis of primary visual photochemistry

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Oligosaccharides

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)