7P3L | pdb_00007p3l

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free:
0.173 (Depositor), 0.174 (DCC)
R-Value Work:
0.151 (Depositor), 0.152 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05326
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UN1 (Subject of Investigation/LOI) Query on UN1 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-AMINOHEXANEDIOIC ACID C₆ H₁₁ N O₄ OYIFNHCXNCRBQI-BYPYZUCNSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
KCY (Subject of Investigation/LOI) Query on KCY Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	D-homocysteine C₄ H₉ N O₂ S FFFHZYDWPBMWHY-GSVOUGTGSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CYS (Subject of Investigation/LOI) Query on CYS Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.173 (Depositor), 0.174 (DCC)
R-Value Work: 0.151 (Depositor), 0.152 (DCC)
R-Value Observed: 0.152 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

Rabe, P.

Clifton, I.

Schofield, C.J.

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