6NKJ | pdb_00006nkj

1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with (2R)-2-(phosphonooxy)propanoic acid.

PDB DOI: https://doi.org/10.2210/pdb6NKJ/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-01-07 Released: 2019-01-16
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.155 (Depositor), 0.160 (DCC)
R-Value Work:
0.145 (Depositor), 0.150 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.

Inniss, N.L., Minasov, G., Chang, C., Tan, K., Kim, Y., Maltseva, N., Stogios, P., Filippova, E., Michalska, K., Osipiuk, J., Jaroszewki, L., Godzik, A., Savchenko, A., Joachimiak, A., Anderson, W.F., Satchell, K.J.F.

(2025) Microbiol Resour Announc 14: e0020025-e0020025

PubMed: 40391899 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/mra.00200-25
Primary Citation of Related Structures:
5TR3, 5TV2, 5TY0, 5U1O, 5U2G, 5U47, 5UE1, 5UME, 5US8, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5V36, 5VDN, 5VFB, 5VH6, 5WI5, 5WP0, 6AON, 6AOO, 6AWA, 6AZI, 6B4O, 6B5F, 6B8D, 6BAL, 6BK7, 6BLB, 6BQ9, 6BZ0, 6C8Q, 6CMZ, 6CN1, 6CZP, 6E5Y, 6MUQ, 6N0I, 6N7F, 6NFP, 6NKJ, 6PO4, 6PU9, 6PUA, 6PXA, 6W2Z, 9BZN, 9BZQ

PubMed Abstract:
Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

Organizational Affiliation

Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 93.25 kDa
Atom Count: 8,928
Modeled Residue Count: 842
Deposited Residue Count: 860
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1	A, B	430	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: murA1, murA, SP_1966 EC: 2.5.1.7
UniProt
Find proteins for Q97NQ4 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q97NQ4 Go to UniProtKB: Q97NQ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q97NQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
0V5 Query on 0V5 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(2R)-2-(phosphonooxy)propanoic acid C₃ H₇ O₆ P CSZRNWHGZPKNKY-UWTATZPHSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.155 (Depositor), 0.160 (DCC)
R-Value Work: 0.145 (Depositor), 0.150 (DCC)
R-Value Observed: 0.145 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36nkj

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.713	α = 90
b = 120.713	β = 90
c = 70.614	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2019-01-16
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary
Version 1.3: 2026-02-11
Changes: Database references