5EKS

Structure of 3-dehydroquinate synthase from Acinetobacter baumannii in complex with NAD

PDB DOI: https://doi.org/10.2210/pdb5EKS/pdb

Classification: LYASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-11-04 Released: 2015-12-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.214
R-Value Work: 0.167
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of 3-dehydroquinate synthase from Acinetobacter baumannii in complex with NAD

Abendroth, J., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 82.5 kDa
Atom Count: 6,141
Modelled Residue Count: 709
Deposited Residue Count: 736
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 synthase	A, B	368	Acinetobacter baumannii	Mutation(s): 0 Gene Names: aroB, AB895_1177, AB988_0958, AB994_2838, ABCIP7010_3378, ABUW_0296, ACX61_01585, IOMTU433_0312, RU84_01465, TE32_01480... aroB, AB895_1177, AB988_0958, AB994_2838, ABCIP7010_3378, ABUW_0296, ACX61_01585, IOMTU433_0312, RU84_01465, TE32_01480, VM83_15710 EC: 4.2.3.4
UniProt
Find proteins for V5V8R5 (Acinetobacter baumannii) Explore V5V8R5 Go to UniProtKB: V5V8R5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V5V8R5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.214
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M35EKS

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.4	α = 90
b = 58.92	β = 97.4
c = 104.81	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-12-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-12-02
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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5EKS

Structure of 3-dehydroquinate synthase from Acinetobacter baumannii in complex with NAD

Structure of 3-dehydroquinate synthase from Acinetobacter baumannii in complex with NAD

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)