7ZQT | pdb_00007zqt

Helicobacter pylori adhesin BabA bound to neutralising human antibody.

PDB DOI: https://doi.org/10.2210/pdb7ZQT/pdb

Classification: CELL ADHESION
Organism(s): Helicobacter pylori, Lama glama, Homo sapiens
Expression System: Escherichia coli, Drosophila melanogaster
Mutation(s): No

Deposited: 2022-05-03 Released: 2023-05-17
Deposition Author(s): Moonens, K., Boren, T.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.281 (Depositor), 0.281 (DCC)
R-Value Work:
0.225 (Depositor), 0.227 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Helicobacter pylori adhesin BabA bound to neutralising human antibody.

Remaut, H.

To be published.

Macromolecule Content

Total Structure Weight: 218.35 kDa
Atom Count: 13,999
Modeled Residue Count: 1,859
Deposited Residue Count: 2,038
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adhesin binding fucosylated histo-blood group antigen	A, E	466	Helicobacter pylori	Mutation(s): 0 Gene Names: babA2
UniProt
Find proteins for O52269 (Helicobacter pylori) Explore O52269 Go to UniProtKB: O52269
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O52269
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody Nb19	B, F	120	Lama glama	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VH domain human IgG antibody ABbA	C, G	222	Homo sapiens	Mutation(s): 0

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VL domain human IgG antibody ABbA	D, H	211	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth E] MOL2 format, chain J [auth A] MOL2 format, chain L [auth E] mmCIF format, chain J [auth A] mmCIF format, chain L [auth E]	J [auth A], L [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth E] Interactions & Density Focus chain J [auth A] Focus chain L [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth E] MOL2 format, chain I [auth A] MOL2 format, chain K [auth E] mmCIF format, chain I [auth A] mmCIF format, chain K [auth E]	I [auth A], K [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth E] Interactions & Density Focus chain I [auth A] Focus chain K [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.281 (Depositor), 0.281 (DCC)
R-Value Work: 0.225 (Depositor), 0.227 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.7	α = 90
b = 68.4	β = 104.4
c = 176.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G033717N

Revision History (Full details and data files)

Version 1.0: 2023-05-17
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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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.