2Z2C | pdb_00002z2c

MURA inhibited by unag-cnicin adduct

PDB DOI: https://doi.org/10.2210/pdb2Z2C/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-05-17 Released: 2008-05-20
Deposition Author(s): Steinbach, A., Skarzynski, T., Scheidig, A.J., Klein, C.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.271 (Depositor), 0.265 (DCC)
R-Value Work:
0.191 (Depositor), 0.189 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

The Antibacterial Target Enzyme Mura Synthesizes its Own Non-Covalent Suicide Inhibitor from the Natural Product Cnicin

Steinbach, A., Skarzynski, T., Scheidig, A.J., Klein, C.D.

To be published.

Macromolecule Content

Total Structure Weight: 184.39 kDa
Atom Count: 13,786
Modeled Residue Count: 1,672
Deposited Residue Count: 1,692
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase	A, B, C, D	423	Escherichia coli	Mutation(s): 0 Gene Names: MURA EC: 2.5.1.7
UniProt
Find proteins for P0A749 (Escherichia coli (strain K12)) Explore P0A749 Go to UniProtKB: P0A749
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A749
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
UDC Query on UDC Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	2-acetamido-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-2-deoxy-alpha-D-glucopyranose C₁₃ H₂₃ N O₁₀ NSPVGDAWQINIKU-TXJFNNIZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.271 (Depositor), 0.265 (DCC)
R-Value Work: 0.191 (Depositor), 0.189 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.127	α = 108.69
b = 80.369	β = 111.07
c = 84.871	γ = 101.17

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MAR345dtb	data collection
MAR345	data collection
XDS	data scaling
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-05-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-05-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-27
Changes: Advisory, Database references, Derived calculations, Non-polymer description
Version 1.3: 2017-10-11
Changes: Advisory, Refinement description
Version 1.4: 2020-06-24
Changes: Advisory, Data collection, Derived calculations
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Derived calculations, Structure summary
Version 1.6: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.7: 2024-10-23
Changes: Structure summary