7OMO | pdb_00007omo

Crystal structure of coelenteramine-bound Renilla reniformis luciferase RLuc8-D120A variant

PDB DOI: https://doi.org/10.2210/pdb7OMO/pdb

Classification: LUMINESCENT PROTEIN
Organism(s): Renilla reniformis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-05-24 Released: 2022-06-01
Deposition Author(s): Schenkmayerova, A., Marek, M.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.181 (Depositor), 0.166 (DCC)
R-Value Work:
0.163 (Depositor), 0.166 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 74.57 kDa
Atom Count: 5,525
Modeled Residue Count: 603
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
Renilla reniformis luciferase RLuc8-D120A variant	A, B	317	Renilla reniformis	Mutation(s): 0 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
VKB (Subject of Investigation/LOI) Query on VKB 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]	4-[5-azanyl-6-(phenylmethyl)pyrazin-2-yl]phenol C₁₇ H₁₅ N₃ O BWNPYAKFDUFNND-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B]	G [auth A], H [auth A], I [auth A], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]