9P1V | pdb_00009p1v

Structure of MAb PhtD3 in complex with PhtD

PDB DOI: https://doi.org/10.2210/pdb9P1V/pdb
EM Map EMD-71135: EMDB EMDataResource

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Streptococcus pneumoniae, Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2025-06-10 Released: 2026-06-17
Deposition Author(s): Du, J., Cui, J., Lin, Z., Eisenhauer, J., Weiner, D.B., Pallesen, J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9P1V

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

Literature

Fc-engineering and structural characterization of a broadly reactive monoclonal antibody targeting the pneumococcal histidine triad protein D (PhtD) on the surface of Streptococcus pneumoniae

Eisenhauer, J., Gingerich, A.D., Du, J., Parzych, E.M., Li, Y., McCormick, A.L., Lin, Z.J., Cui, J., Cassel, J., Bhardwaj, B., Chu, J.D., Smith, T., Patel, A., Mousa, J.J., Pallesen, J., Weiner, D.B.

To be published.

Macromolecule Content

Total Structure Weight: 171.51 kDa
Atom Count: 4,086
Modeled Residue Count: 532
Deposited Residue Count: 1,547
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad protein D	A	838	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: phtD
UniProt
Find proteins for A0A0E3JFL0 (Streptococcus pneumoniae) Explore A0A0E3JFL0 Go to UniProtKB: A0A0E3JFL0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0E3JFL0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MAb PhtD3 antibody light chain	B [auth L]	235	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MAb PhtD3 antibody heavy chain	C [auth H]	474	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI141236

Revision History (Full details and data files)

Version 1.0: 2026-06-17
Type: Initial release