5TL8 | pdb_00005tl8

Naegleria fowleri CYP51-posaconazole complex

• PDB DOI: https://doi.org/10.2210/pdb5TL8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Naegleria fowleri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-10 Released: 2017-10-11 
• Deposition Author(s): Podust, L.M., Jennings, G., Calvet-Alvarez, C., Debnath, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.249 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of the Naegleria fowleri CYP51 at 1.7 Angstroms resolution

Podust, L.M., Jennings, G., Calvet-Alvarez, C., Debnath, A.

To be published.

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: 55.3 kDa 
• Atom Count: 3,884 
• Modeled Residue Count: 450 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein CYP51	A	466	Naegleria fowleri	Mutation(s): 0  Gene Names: NF0102700
UniProt
Find proteins for A0A2H4A2U9 (Naegleria fowleri) Explore A0A2H4A2U9  Go to UniProtKB:  A0A2H4A2U9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X2N	C [auth A]	POSACONAZOLE C37 H42 F2 N8 O4 RAGOYPUPXAKGKH-XAKZXMRKSA-N
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.249 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.03	α = 90
b = 55.04	β = 100.07
c = 71.62	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Podust, L.M., Jennings, G., Calvet-Alvarez, C., Debnath, A.

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary