6E5Y | pdb_00006e5y

1.50 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis in Complex with AMP.

PDB DOI: https://doi.org/10.2210/pdb6E5Y/pdb

Classification: HYDROLASE
Organism(s): Bordetella pertussis Tohama I
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-07-23 Released: 2018-08-01
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Cardona-Correa, A., 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: 1.50 Å
R-Value Free:
0.179 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.160 (DCC)
R-Value Observed:
0.156 (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

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: 50.65 kDa
Atom Count: 4,564
Modeled Residue Count: 438
Deposited Residue Count: 448
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Argininosuccinate synthase	A	448	Bordetella pertussis Tohama I	Mutation(s): 0 Gene Names: argG, BP3537 EC: 6.3.4.5
UniProt
Find proteins for Q7VTJ9 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VTJ9 Go to UniProtKB: Q7VTJ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7VTJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP 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]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.179 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.160 (DCC)
R-Value Observed: 0.156 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36e5y

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.287	α = 90
b = 97.287	β = 90
c = 93.2	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-08-01
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2026-02-11
Changes: Database references, Structure summary

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Deposit Data

Help and Resources

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1.50 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis in Complex with AMP.

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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