7OMD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coelenterazine h 2-monooxygenase
A, B
317Renilla reniformisMutation(s): 1 
EC: 1.13.12.5
UniProt
Find proteins for P27652 (Renilla reniformis)
Explore P27652 
Go to UniProtKB:  P27652
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27652
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VK8 (Subject of Investigation/LOI)
Query on VK8

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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
PEG (Subject of Investigation/LOI)
Query on PEG

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E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS (Subject of Investigation/LOI)
Query on DMS

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D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

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I [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.569α = 90
b = 84.057β = 90.72
c = 77.437γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionCzech RepublicMSCA-IF-2017 792772

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description