9PMN | pdb_00009pmn

Crystal structure of Capsular polysaccharide biosynthesis protein from Bordetella pertussis in complex with NAD and uridine-diphosphate-n-acetylgalactosamine

PDB DOI: https://doi.org/10.2210/pdb9PMN/pdb

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

Deposited: 2025-07-18 Released: 2025-08-06
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, 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: 2.40 Å
R-Value Free:
0.247 (Depositor), 0.251 (DCC)
R-Value Work:
0.193 (Depositor), 0.200 (DCC)
R-Value Observed:
0.196 (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 Capsular polysaccharide biosynthesis protein from Bordetella pertussis in complex with NAD and uridine-diphosphate-n-acetylgalactosamine

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

To be published.

Macromolecule Content

Total Structure Weight: 158.97 kDa
Atom Count: 11,119
Modeled Residue Count: 1,358
Deposited Residue Count: 1,392
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsular polysaccharide biosynthesis protein	A, B, C, D	348	Bordetella pertussis Tohama I	Mutation(s): 0 Gene Names: wbpP, tviC, vipB, BP1630, BP3149
UniProt
Find proteins for Q7TTK0 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7TTK0 Go to UniProtKB: Q7TTK0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7TTK0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B], R [auth C], W [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain W [auth D]
UD2 (Subject of Investigation/LOI) Query on UD2 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	H [auth A], O [auth B], S [auth C], X [auth D]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-NESSUJCYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain X [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	I [auth A] J [auth A] K [auth A] P [auth B] T [auth C] I [auth A], J [auth A], K [auth A], P [auth B], T [auth C], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain Y [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	E [auth A] F [auth A] L [auth B] M [auth B] Q [auth C] E [auth A], F [auth A], L [auth B], M [auth B], Q [auth C], U [auth D], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.247 (Depositor), 0.251 (DCC)
R-Value Work: 0.193 (Depositor), 0.200 (DCC)
R-Value Observed: 0.196 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39PMN

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.726	α = 90
b = 155.942	β = 93.17
c = 79.958	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: 2025-08-06

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

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