7ZIC

Crystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of CYP125 from Mycobacterium tuberculosis in complex with an inhibitor

Kavanagh, M.Snee, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid C26-monooxygenase
A, B, C
418Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: cyp125cyp125A1Rv3545cMTCY03C7.11
EC: 1.14.15.29
UniProt
Find proteins for P9WPP1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP1 
Go to UniProtKB:  P9WPP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
T [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
5YG (Subject of Investigation/LOI)
Query on 5YG

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E [auth A],
L [auth B],
S [auth C]
~{N}-[(4-methoxyphenyl)methyl]-4-(pyridin-4-ylmethyl)aniline
C20 H20 N2 O
FVAKBCRCJCQWCW-UHFFFAOYSA-N
SO4
Query on SO4

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AA [auth C]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
AA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth C],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.233α = 90
b = 68.684β = 93.968
c = 144.472γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description