4CNP | pdb_00004cnp

Structure of the Salmonella typhi type I dehydroquinase inhibited by a 3-epiquinic acid derivative

PDB DOI: https://doi.org/10.2210/pdb4CNP/pdb

Classification: LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-01-23 Released: 2015-02-18
Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Lence, E., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.160 (Depositor), 0.170 (DCC)
R-Value Work:
0.133 (Depositor), 0.140 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Mechanistic Insight Into the Reaction Catalyzed by Type I Dehydroquinase

Maneiro, M., Peon, A., Lence, E., Otero, J.M., Llamas-Saiz, A.L., van Raaij, M.J., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C.

To be published.

Macromolecule Content

Total Structure Weight: 55.97 kDa
Atom Count: 4,901
Modelled Residue Count: 504
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B	252	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0 EC: 4.2.1.10
UniProt
Find proteins for P24670 (Salmonella typhi) Explore P24670 Go to UniProtKB: P24670
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24670
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9C4 Query on 9C4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	(2S)-2-HYDROXY-3-EPIQUINIC ACID C₇ H₁₂ O₇ OLBQNCISLUABGO-LNHNIDQWSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.160 (Depositor), 0.170 (DCC)
R-Value Work: 0.133 (Depositor), 0.140 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.216	α = 90
b = 44.473	β = 95.2
c = 84.702	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-18
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Structure of the Salmonella typhi type I dehydroquinase inhibited by a 3-epiquinic acid derivative

Mechanistic Insight Into the Reaction Catalyzed by Type I Dehydroquinase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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