6X7W | pdb_00006x7w

Vaccine-elicited mouse FP-targeting neutralizing antibody vFP49.02 in complex with HIV fusion peptide (residue 512-519)

PDB DOI: https://doi.org/10.2210/pdb6X7W/pdb

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Mus musculus, Human immunodeficiency virus 1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-05-30 Released: 2021-06-02
Deposition Author(s): Xu, K., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.248 (Depositor), 0.250 (DCC)
R-Value Work:
0.214 (Depositor), 0.216 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Distinct Classes of HIV-1 Cross-Clade Neutralizing Antibodies Targeting Fusion Peptide Elicited in Mice by Diverse Immunization Regimens

Xu, K., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 98.99 kDa
Atom Count: 7,550
Modeled Residue Count: 886
Deposited Residue Count: 916
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody vFP49.02 heavy chain	A, C [auth H]	235	Mus musculus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV fusion peptide 512-519	B [auth G], F [auth D]	9	Human immunodeficiency virus 1	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody vFP49.02 light chain	D [auth L], E [auth C]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain G [auth L] MOL2 format, chain H [auth C] MOL2 format, chain G [auth L] mmCIF format, chain H [auth C] mmCIF format, chain G [auth L]	G [auth L], H [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth L] Focus chain H [auth C] Interactions & Density Focus chain G [auth L] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.248 (Depositor), 0.250 (DCC)
R-Value Work: 0.214 (Depositor), 0.216 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.881	α = 90
b = 99.229	β = 90
c = 137.9	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-06-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-02
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, 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.