11BL | pdb_000011bl

Crystal Structure of a Ribokinase from Brucella suis in complex ADP (P21 form)

PDB DOI: https://doi.org/10.2210/pdb11BL/pdb

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

Deposited: 2026-02-16 Released: 2026-02-25
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: 2.90 Å
R-Value Free:
0.286 (Depositor), 0.288 (DCC)
R-Value Work:
0.245 (Depositor), 0.249 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of a Ribokinase from Brucella suis in complex ADP (P21 form)

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

To be published.

Macromolecule Content

Total Structure Weight: 130.8 kDa
Atom Count: 8,193
Modeled Residue Count: 1,186
Deposited Residue Count: 1,248
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	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 E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A], G [auth B], K [auth C], M [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain M [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain N [auth D]	H [auth B], I [auth B], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C]	F [auth A], J [auth B], L [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.286 (Depositor), 0.288 (DCC)
R-Value Work: 0.245 (Depositor), 0.249 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.363	α = 90
b = 81.851	β = 106.31
c = 100.634	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-25

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