6RGE | pdb_00006rge

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with an inhibitor

PDB DOI: https://doi.org/10.2210/pdb6RGE/pdb

Classification: TRANSFERASE
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-04-16 Released: 2020-05-13
Deposition Author(s): Gelin, M., Labesse, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.201 (Depositor), 0.202 (DCC)
R-Value Observed:
0.202 (Depositor)

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Literature

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with an inhibitor

Gelin, M., Labesse, G.

To be published.

Macromolecule Content

Total Structure Weight: 31.89 kDa
Atom Count: 2,240
Modeled Residue Count: 259
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD kinase 1	A	272	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: nadK1, lmo0968 EC: 2.7.1.23
UniProt
Find proteins for Q8Y8D7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y8D7 Go to UniProtKB: Q8Y8D7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y8D7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K1Z Query on K1Z 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]	[(2~{R},3~{R},4~{R},5~{R})-2-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]prop-1-ynyl]-6-azanyl-purin-9-yl]-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] dihydrogen phosphate C₂₃ H₂₇ N₁₀ O₁₁ P KWDXFYHXTKUVMJ-MKWZPUSRSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CIT Query on CIT 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]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223 (Depositor), 0.223 (DCC)
R-Value Work: 0.201 (Depositor), 0.202 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.08	α = 90
b = 75.22	β = 90
c = 118.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references, Refinement description

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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.