4G46 | pdb_00004g46

Structure of cytochrome P450 CYP121 in complex with 4-oxo-4,5,6,7-tetrahydrobenzofuran-3-carboxylate

• PDB DOI: https://doi.org/10.2210/pdb4G46/pdb

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


• Deposited: 2012-07-16 Released: 2012-09-05 
• Deposition Author(s): Hudson, S.A., McLean, K.J., Surade, S., Yang, Y.-Q., Leys, D., Ciulli, A., Munro, A.W., Abell, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Application of Fragment Screening and Merging to the Discovery of Inhibitors of the Mycobacterium tuberculosis Cytochrome P450 CYP121

Hudson, S.A., McLean, K.J., Surade, S., Yang, Y.-Q., Leys, D., Ciulli, A., Munro, A.W., Abell, C.

(2012) Angew Chem Int Ed Engl 51: 9311-9316

• PubMed: 22890978 
• DOI: https://doi.org/10.1002/anie.201202544
• Primary Citation Related Structures: 
  4G1X, 4G2G, 4G44, 4G45, 4G46, 4G47, 4G48

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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.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.49 kDa 
• Atom Count: 3,886 
• Modeled Residue Count: 395 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 121	A	396	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: Rv2276 EC: 1.14 (PDB Primary Data), 1.14.19.70 (UniProt)
UniProt
Find proteins for P9WPP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPP7  Go to UniProtKB:  P9WPP7

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
TTY	G [auth A]	4-oxo-4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid C9 H8 O4 FABBWECRHZNMDQ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.57	α = 90
b = 77.57	β = 90
c = 262.99	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Hudson, S.A., McLean, K.J., Surade, S., Yang, Y.-Q., Leys, D., Ciulli, A., Munro, A.W., Abell, C.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2012-09-19
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations