9TPY | pdb_00009tpy

HomA ectodomain (EDC-HomA)

PDB DOI: https://doi.org/10.2210/pdb9TPY/pdb

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

Deposited: 2025-12-19 Released: 2026-08-19
Deposition Author(s): Rodriguez-Banqueri, A., Goulas, T., Eckhard, U., Gomis-Ruth, F.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.266 (Depositor), 0.259 (DCC)
R-Value Work:
0.241 (Depositor), 0.241 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9TPY

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

Literature

Structure of HomA ectodomain at 2.85Anstrongs resolution

Rodriguez-Banqueri, A., Goulas, T., Eckhard, U., Gomis-Ruth, F.X.

To be published.

Macromolecule Content

Total Structure Weight: 439.08 kDa
Atom Count: 24,235
Modeled Residue Count: 3,205
Deposited Residue Count: 3,896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HomA	A, B, C, D, E A, B, C, D, E, F, G, H	487	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: HP_0710
UniProt
Find proteins for O25414 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25414 Go to UniProtKB: O25414
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O25414
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain EB [auth H] SDF format, chain FA [auth D] SDF format, chain TA [auth F] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain TA [auth F] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth H] mmCIF format, chain FA [auth D] mmCIF format, chain TA [auth F]	EA [auth D], EB [auth H], FA [auth D], TA [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain TA [auth F] Interactions & Density Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain TA [auth F]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth G] SDF format, chain BA [auth C] SDF format, chain BB [auth G] SDF format, chain CA [auth C] SDF format, chain CB [auth G] SDF format, chain FB [auth H] SDF format, chain GA [auth D] SDF format, chain GB [auth H] SDF format, chain HA [auth D] SDF format, chain HB [auth H] SDF format, chain IA [auth D] SDF format, chain IB [auth H] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain ZA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain FB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth H] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth G] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth G] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth G] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth G] mmCIF format, chain FB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain HB [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth H] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth G]	AA [auth C] AB [auth G] BA [auth C] BB [auth G] CA [auth C] AA [auth C], AB [auth G], BA [auth C], BB [auth G], CA [auth C], CB [auth G], FB [auth H], GA [auth D], GB [auth H], HA [auth D], HB [auth H], IA [auth D], IB [auth H], JA [auth D], K [auth A], KA [auth D], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth E], PA [auth E], QA [auth E], R [auth B], RA [auth E], S [auth B], T [auth B], U [auth B], UA [auth F], V [auth B], VA [auth F], WA [auth F], XA [auth F], Y [auth C], Z [auth C], ZA [auth G]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C] Focus chain ZA [auth G]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain MA [auth E] SDF format, chain X [auth C] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain X [auth C] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain X [auth C]	J [auth A], MA [auth E], X [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain MA [auth E] Focus chain X [auth C] Interactions & Density Focus chain J [auth A] Focus chain MA [auth E] Focus chain X [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain DB [auth H] SDF format, chain I [auth A] SDF format, chain LA [auth E] SDF format, chain P [auth B] SDF format, chain SA [auth F] SDF format, chain W [auth C] SDF format, chain YA [auth G] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain YA [auth G] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain I [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain W [auth C] mmCIF format, chain YA [auth G]	DA [auth D] DB [auth H] I [auth A] LA [auth E] P [auth B] DA [auth D], DB [auth H], I [auth A], LA [auth E], P [auth B], SA [auth F], W [auth C], YA [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain DB [auth H] Focus chain I [auth A] Focus chain LA [auth E] Focus chain P [auth B] Focus chain SA [auth F] Focus chain W [auth C] Focus chain YA [auth G] Interactions & Density Focus chain DA [auth D] Focus chain DB [auth H] Focus chain I [auth A] Focus chain LA [auth E] Focus chain P [auth B] Focus chain SA [auth F] Focus chain W [auth C] Focus chain YA [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain NA [auth E] MOL2 format, chain NA [auth E] mmCIF format, chain NA [auth E]	NA [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain NA [auth E] Interactions & Density Focus chain NA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.266 (Depositor), 0.259 (DCC)
R-Value Work: 0.241 (Depositor), 0.241 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.9	α = 84.5
b = 126.6	β = 84.4
c = 155.1	γ = 83.5

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
TNT	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-19

Deposition Author(s):

Rodriguez-Banqueri, A.

Gomis-Ruth, F.X.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-08-19
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.