9YL5 | pdb_00009yl5

Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 5-amino-6-(D-ribitylamino)uracil

PDB DOI: https://doi.org/10.2210/pdb9YL5/pdb

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

Deposited: 2025-10-08 Released: 2025-10-22
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: 2.56 Å
R-Value Free:
0.248 (Depositor), 0.253 (DCC)
R-Value Work:
0.201 (Depositor), 0.208 (DCC)
R-Value Observed:
0.203 (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 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 5-amino-6-(D-ribitylamino)uracil

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

To be published.

Macromolecule Content

Total Structure Weight: 88.68 kDa
Atom Count: 5,652
Modeled Residue Count: 765
Deposited Residue Count: 815
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A, B, C, D, E	163	Bordetella pertussis Tohama I	Mutation(s): 0 Gene Names: ribH, BP3485 EC: 2.5.1.78
UniProt
Find proteins for Q7VTN4 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VTN4 Go to UniProtKB: Q7VTN4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7VTN4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMZ (Subject of Investigation/LOI) Query on LMZ Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	BA [auth E], L [auth A], P [auth B], T [auth C], X [auth D]	5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE C₉ H₁₄ N₄ O₇ YMWIHKCBRFEJMH-RPDRRWSUSA-N		Interactions Focus chain BA [auth E] Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	AA [auth E] F [auth A] G [auth A] H [auth A] I [auth A] AA [auth E], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D], Y [auth E], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.248 (Depositor), 0.253 (DCC)
R-Value Work: 0.201 (Depositor), 0.208 (DCC)
R-Value Observed: 0.203 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39YL5

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.126	α = 90
b = 75.061	β = 105.57
c = 180.117	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: 2025-10-22

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