5GYZ | pdb_00005gyz

luciferase AMP/7-cy-L complex

PDB DOI: https://doi.org/10.2210/pdb5GYZ/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.
Funding Organization(s): National Program on Key Basic Research Project of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of luciferase with AMP/7-cy-L at 2.4 Angstroms resolution

Chao, T.Z., Su, J.

To be published.

Macromolecule Content

Total Structure Weight: 49.51 kDa
Atom Count: 3,681
Modeled Residue Count: 431
Deposited Residue Count: 435
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	435	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 4 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]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]