5DWV | pdb_00005dwv

Crystal structure of the Luciferase complexed with substrate analogue

PDB DOI: https://doi.org/10.2210/pdb5DWV/pdb

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

Deposited: 2015-09-23 Released: 2016-09-28
Deposition Author(s): Su, J., Li, Z., Yuan, Z., Gu, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the Luciferase complexed with substrate analogue

Su, J., Li, Z., Yuan, Z., Gu, L.

To be published.

Macromolecule Content

Total Structure Weight: 63.67 kDa
Atom Count: 3,662
Modeled Residue Count: 431
Deposited Residue Count: 573
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	573	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
5J4 Query on 5J4 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]	2-[6-(cyclobuta-1,3-dien-1-ylamino)-1,3-benzothiazol-2-yl]-1,3-thiazol-4-ol C₁₄ H₉ N₃ O S₂ AMUPGDQXMKYKJQ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.101	α = 90
b = 73.101	β = 90
c = 96.465	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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.