7OMD | pdb_00007omd

Crystal structure of azacoelenterazine-bound Renilla reniformis luciferase variant RLuc8-D162A

PDB DOI: https://doi.org/10.2210/pdb7OMD/pdb

Classification: LUMINESCENT PROTEIN
Organism(s): Renilla reniformis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-05-21 Released: 2022-06-01
Deposition Author(s): Schenkmayerova, A., Janin, Y.L., Marek, M.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.211 (Depositor), 0.212 (DCC)
R-Value Work:
0.176 (Depositor), 0.177 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Catalytic mechanism for Renilla-type luciferases

Schenkmayerova, A., Toul, M., Pluskal, D., Baatallah, R., Gagnot, G., Pinto, G.P., Santana, V.T., Stuchla, M., Neugebauer, P., Chaiyen, P., Damborsky, J., Bednar, D., Janin, Y.L., Prokop, Z., Marek, M.

(2023) Nat Catal

DOI: https://doi.org/10.1038/s41929-022-00895-z

Macromolecule Content

Total Structure Weight: 75.72 kDa
Atom Count: 5,955
Modeled Residue Count: 619
Deposited Residue Count: 634
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coelenterazine h 2-monooxygenase	A, B	317	Renilla reniformis	Mutation(s): 1 EC: 1.13.12.5
UniProt
Find proteins for P27652 (Renilla reniformis) Explore P27652 Go to UniProtKB: P27652
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27652
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VK8 (Subject of Investigation/LOI) Query on VK8 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], F [auth B], G [auth B], H [auth B]	6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-8-(phenylmethyl)-[1,2,4]triazolo[4,3-a]pyrazin-3-one C₂₅ H₂₀ N₄ O₃ FAFQJYQLYIUGAT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS (Subject of Investigation/LOI) Query on DMS 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]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]