4KTJ

Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4-(3-amino-1H-pyrazol-4-yl)phenol

• PDB DOI: https://doi.org/10.2210/pdb4KTJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-20 Released: 2013-07-03 
• Deposition Author(s): Hudson, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.195 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Overcoming the Limitations of Fragment Merging: Rescuing a Strained Merged Fragment Series Targeting Mycobacterium tuberculosis CYP121.

Hudson, S.A., Surade, S., Coyne, A.G., McLean, K.J., Leys, D., Munro, A.W., Abell, C.

(2013) ChemMedChem 8: 1451-1456

• PubMed: 23788280 
• DOI: https://doi.org/10.1002/cmdc.201300219
• Primary Citation of Related Structures:  
  4KTF, 4KTJ, 4KTK, 4KTL

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Organizational Affiliation: 

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.16 kDa 
• Atom Count: 3,618 
• Modelled Residue Count: 394 
• Deposited Residue Count: 395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 121	A	395	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv2276, RVBD_2276 EC: 1.14

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
KTJ	E [auth A]	4-(3-amino-1H-pyrazol-4-yl)phenol C9 H9 N3 O WRERTDQKTDJJIZ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.195 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.03	α = 90
b = 78.03	β = 90
c = 265.161	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Hudson, S.A.

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description