5GZ2 | pdb_00005gz2

luciferase complex with 7-cy-L

PDB DOI: https://doi.org/10.2210/pdb5GZ2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Photinus pyralis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-09-26 Released: 2017-09-27
Deposition Author(s): Su, J., Wang, F., Gu, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.239 (Depositor), 0.246 (DCC)
R-Value Work:
0.208 (Depositor), 0.219 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5GZ2

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

luciferase complex with 7-cy-L

Su, J., Wang, F.

To be published.

Macromolecule Content

Total Structure Weight: 48.89 kDa
Atom Count: 3,536
Modeled Residue Count: 432
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Luciferin 4-monooxygenase	A	436	Photinus pyralis	Mutation(s): 0 EC: 1.13.12.7
UniProt
Find proteins for P08659 (Photinus pyralis) Explore P08659 Go to UniProtKB: P08659
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08659
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7BV Query on 7BV Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4S)-2-[6-(azepan-1-yl)-1,3-benzothiazol-2-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid C₁₇ H₁₉ N₃ O₂ S₂ GRFYBXURSQOJAN-CYBMUJFWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.239 (Depositor), 0.246 (DCC)
R-Value Work: 0.208 (Depositor), 0.219 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.154	α = 90
b = 74.154	β = 90
c = 95.622	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.