7P3L

Isopenicillin N synthase in complex with Fe and the substrate analogue AadCyshomoCys

• PDB DOI: https://doi.org/10.2210/pdb7P3L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus nidulans FGSC A4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-08 Released: 2022-07-20 
• Deposition Author(s): Rabe, P., Clifton, I., Schofield, C.J.
• Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom), Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.173 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

Starting Model: experimental

Literature

Isopenicillin N synthase in complex with Fe and the substrate analogue AadCyshomoCys

Rabe, P., Clifton, I., Schofield, C.J.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.51 kDa 
• Atom Count: 3,179 
• Modelled Residue Count: 329 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isopenicillin N synthase	A	331	Aspergillus nidulans FGSC A4	Mutation(s): 0  Gene Names: ipnA, ips, AN2622 EC: 1.21.3.1
UniProt
Find proteins for P05326 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore P05326  Go to UniProtKB:  P05326

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UN1 (Subject of Investigation/LOI)	H [auth A]	2-AMINOHEXANEDIOIC ACID C6 H11 N O4 OYIFNHCXNCRBQI-BYPYZUCNSA-N
KCY (Subject of Investigation/LOI)	J [auth A]	D-homocysteine C4 H9 N O2 S FFFHZYDWPBMWHY-GSVOUGTGSA-N
CYS (Subject of Investigation/LOI)	I [auth A]	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.173 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.98	α = 90
b = 71.42	β = 90
c = 101.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): Rabe, P., Clifton, I., Schofield, C.J.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106244/Z/14/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	106244/Z/14/Z
Wellcome Trust	United Kingdom	210734/Z/18/Z
Royal Society	United Kingdom	RSWF/R2/182017

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2024-01-31
  Changes: Refinement description