9ZPU | pdb_00009zpu

Crystal Structure of a Ribokinase from Brucella suis in complex with ADP

PDB DOI: https://doi.org/10.2210/pdb9ZPU/pdb

Classification: TRANSFERASE
Organism(s): Brucella suis 1330
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-12-17 Released: 2025-12-31
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.259 (Depositor), 0.258 (DCC)
R-Value Work:
0.195 (Depositor), 0.199 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of a Ribokinase from Brucella suis in complex with ADP

Seibold, S., Lovell, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 199.72 kDa
Atom Count: 13,412
Modeled Residue Count: 1,830
Deposited Residue Count: 1,872
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B, C, D, E A, B, C, D, E, F	312	Brucella suis 1330	Mutation(s): 0 Gene Names: rbsK, BS1330_II0005 EC: 2.7.1.15
UniProt
Find proteins for A0A0H3GDY9 (Brucella suis biovar 1 (strain 1330)) Explore A0A0H3GDY9 Go to UniProtKB: A0A0H3GDY9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3GDY9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CB [auth F] SDF format, chain G [auth A] SDF format, chain LA [auth D] SDF format, chain Q [auth B] SDF format, chain TA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain G [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain TA [auth E] mmCIF format, chain BA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain G [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain TA [auth E]	BA [auth C] CB [auth F] G [auth A] LA [auth D] Q [auth B] BA [auth C], CB [auth F], G [auth A], LA [auth D], Q [auth B], TA [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth C] Focus chain CB [auth F] Focus chain G [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain TA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain CB [auth F] Focus chain G [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain TA [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain DB [auth F] SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain FA [auth C] SDF format, chain FB [auth F] SDF format, chain GA [auth C] SDF format, chain GB [auth F] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain HB [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth F] SDF format, chain J [auth A] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain W [auth B] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain Y [auth B] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] SDF format, chain V [auth B] SDF format, chain NA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain NA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth F] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth F] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain ZA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain NA [auth D]	CA [auth C] DA [auth C] DB [auth F] EA [auth C] EB [auth F] CA [auth C], DA [auth C], DB [auth F], EA [auth C], EB [auth F], FA [auth C], FB [auth F], GA [auth C], GB [auth F], H [auth A], HA [auth C], HB [auth F], I [auth A], IA [auth C], IB [auth F], J [auth A], JB [auth F], K [auth A], L [auth A], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], QA [auth D], R [auth B], RA [auth D], S [auth B], T [auth B], U [auth B], UA [auth E], V [auth B], VA [auth E], W [auth B], WA [auth E], X [auth B], XA [auth E], Y [auth B], YA [auth E], ZA [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain ZA [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth F] SDF format, chain BB [auth F] SDF format, chain KA [auth D] SDF format, chain Z [auth C] SDF format, chain SA [auth E] SDF format, chain JA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain KA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain SA [auth E] MOL2 format, chain JA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth F] mmCIF format, chain BB [auth F] mmCIF format, chain KA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain SA [auth E] mmCIF format, chain JA [auth D]	AA [auth C] AB [auth F] BB [auth F] JA [auth D] KA [auth D] AA [auth C], AB [auth F], BB [auth F], JA [auth D], KA [auth D], SA [auth E], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BB [auth F] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain SA [auth E] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BB [auth F] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain SA [auth E] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.259 (Depositor), 0.258 (DCC)
R-Value Work: 0.195 (Depositor), 0.199 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.093	α = 90
b = 138.228	β = 107.04
c = 80.872	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394