1Q1Y

Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin

PDB DOI: https://doi.org/10.2210/pdb1Q1Y/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-07-23 Released: 2004-07-23
Deposition Author(s): Yoon, H.J., Lee, S.K., Kim, H.L., Kim, H.W., Kim, H.W., Lee, J.Y., Mikami, B., Suh, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.235 (Depositor), 0.232 (DCC)
R-Value Work:
0.205 (Depositor), 0.197 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent

Yoon, H.J., Kim, H.L., Lee, S.K., Kim, H.W., Kim, H.W., Lee, J.Y., Mikami, B., Suh, S.W.

(2004) Proteins 57: 639-642

PubMed: 15382235 Search on PubMed
DOI: https://doi.org/10.1002/prot.20231
Primary Citation of Related Structures:
1IX1, 1Q1Y

Organizational Affiliation

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 22.14 kDa
Atom Count: 1,749
Modelled Residue Count: 186
Deposited Residue Count: 191
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	191	Staphylococcus aureus	Mutation(s): 1 Gene Names: SA1100 EC: 3.5.1.88
UniProt
Find proteins for P68826 (Staphylococcus aureus) Explore P68826 Go to UniProtKB: P68826
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68826
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BB2 Query on BB2 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACTINONIN C₁₉ H₃₅ N₃ O₅ XJLATMLVMSFZBN-VYDXJSESSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
BB2	BindingDB: 1Q1Y	IC50: min: 5, max: 20 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.235 (Depositor), 0.232 (DCC)
R-Value Work: 0.205 (Depositor), 0.197 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.417	α = 90
b = 120.844	β = 90
c = 48.057	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-07-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-07-23
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-02-08
Changes: Other, Version format compliance
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary