2KMN | pdb_00002kmn

Solution structure of peptide deformylase complexed with actinonin

PDB DOI: https://doi.org/10.2210/pdb2KMN/pdb

Classification: HYDROLASE/ANTIBIOTIC
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-08-01 Released: 2009-08-25
Deposition Author(s): McElroy, C.A., Amero, C.D., Byerly, D.W., Foster, M.P.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

Validation slider image for 2KMN

This is version 1.3 of the entry. See complete history.

Literature

Solution Structure of Peptide Deformylase complexed with Actinonin

McElroy, C.A., Amero, C.D., Byerly, D.W., Foster, M.P.

To be published.

Macromolecule Content

Total Structure Weight: 17.11 kDa
Atom Count: 1,194
Modeled Residue Count: 147
Deposited Residue Count: 147
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	147	Escherichia coli K-12	Mutation(s): 0 Gene Names: def, fms, b3287, JW3248 EC: 3.5.1.88
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12)) Explore P0A6K3 Go to UniProtKB: P0A6K3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6K3
Sequence Annotations Expand
Reference Sequence

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]
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]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-08-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2022-03-16
Changes: Database references, Derived calculations
Version 1.3: 2024-05-22
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.