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), 0.250 (DCC)
R-Value Work:
0.208 (Depositor), 0.220 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.250 (DCC)
R-Value Work: 0.208 (Depositor), 0.220 (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

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 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.