9S33 | pdb_00009s33

Crystal structure of inhibitor-bound Helicobacter pylori urease

PDB DOI: https://doi.org/10.2210/pdb9S33/pdb

Classification: CELL INVASION
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2025-07-23 Released: 2026-09-09
Deposition Author(s): Chen, X., Luecke, H., Buitrago, A.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.175 (Depositor), 0.175 (DCC)
R-Value Work:
0.137 (Depositor), 0.137 (DCC)
R-Value Observed:
0.139 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structures of inhibitor-bound Helicobacter pylori urease

Chen, X., Buitrago, A., Luecke, H.

To be published.

Macromolecule Content

Total Structure Weight: 534.24 kDa
Atom Count: 43,259
Modeled Residue Count: 4,842
Deposited Residue Count: 4,842
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease subunit alpha	A, C, E, G, I A, C, E, G, I, K	238	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: ureA, hpuA, HP_0073 EC: 3.5.1.5
UniProt
Find proteins for P14916 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P14916 Go to UniProtKB: P14916
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14916
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease subunit beta	B, D, F, H, J B, D, F, H, J, L	569	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: ureB, hpuB, HP_0072 EC: 3.5.1.5
UniProt
Find proteins for P69996 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P69996 Go to UniProtKB: P69996
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69996
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FIA (Subject of Investigation/LOI) Query on FIA Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain V [auth F] SDF format, chain S [auth D] SDF format, chain O [auth B] SDF format, chain HA [auth L] SDF format, chain DA [auth J] MOL2 format, chain Z [auth H] MOL2 format, chain V [auth F] MOL2 format, chain S [auth D] MOL2 format, chain O [auth B] MOL2 format, chain HA [auth L] MOL2 format, chain DA [auth J] mmCIF format, chain Z [auth H] mmCIF format, chain V [auth F] mmCIF format, chain S [auth D] mmCIF format, chain O [auth B] mmCIF format, chain HA [auth L] mmCIF format, chain DA [auth J]	DA [auth J] HA [auth L] O [auth B] S [auth D] V [auth F] DA [auth J], HA [auth L], O [auth B], S [auth D], V [auth F], Z [auth H]	2-{[4-(4-fluorophenyl)-5-(1H-indol-3-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}-N-hydroxyacetamide C₁₈ H₁₄ F N₅ O₂ S MERURASHTKLQBC-UHFFFAOYSA-N		Interactions Focus chain DA [auth J] Focus chain HA [auth L] Focus chain O [auth B] Focus chain S [auth D] Focus chain V [auth F] Focus chain Z [auth H] Interactions & Density Focus chain DA [auth J] Focus chain HA [auth L] Focus chain O [auth B] Focus chain S [auth D] Focus chain V [auth F] Focus chain Z [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain EA [auth K] MOL2 format, chain P [auth C] MOL2 format, chain EA [auth K] mmCIF format, chain P [auth C] mmCIF format, chain EA [auth K]	EA [auth K], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth K] Focus chain P [auth C] Interactions & Density Focus chain EA [auth K] Focus chain P [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth G] SDF format, chain AA [auth H] MOL2 format, chain W [auth G] MOL2 format, chain AA [auth H] mmCIF format, chain W [auth G] mmCIF format, chain AA [auth H]	AA [auth H], W [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth H] Focus chain W [auth G] Interactions & Density Focus chain AA [auth H] Focus chain W [auth G]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain X [auth H] SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain GA [auth L] SDF format, chain FA [auth L] SDF format, chain CA [auth J] SDF format, chain BA [auth J] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth H] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain GA [auth L] MOL2 format, chain FA [auth L] MOL2 format, chain CA [auth J] MOL2 format, chain BA [auth J] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth H] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain GA [auth L] mmCIF format, chain FA [auth L] mmCIF format, chain CA [auth J] mmCIF format, chain BA [auth J]	BA [auth J] CA [auth J] FA [auth L] GA [auth L] M [auth B] BA [auth J], CA [auth J], FA [auth L], GA [auth L], M [auth B], N [auth B], Q [auth D], R [auth D], T [auth F], U [auth F], X [auth H], Y [auth H]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain BA [auth J] Focus chain CA [auth J] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth F] Focus chain U [auth F] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain BA [auth J] Focus chain CA [auth J] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth F] Focus chain U [auth F] Focus chain X [auth H] Focus chain Y [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	B, D, F, H, J B, D, F, H, J, L	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.175 (Depositor), 0.175 (DCC)
R-Value Work: 0.137 (Depositor), 0.137 (DCC)
R-Value Observed: 0.139 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.36	α = 90
b = 181.97	β = 90
c = 186.28	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	FG19020

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.