9MZ6 | pdb_00009mz6

Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the HIV-1 5768-p27 envelope (Env) glycoprotein

PDB DOI: https://doi.org/10.2210/pdb9MZ6/pdb

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

Deposited: 2025-01-22 Released: 2026-01-21
Deposition Author(s): Fetics, S., Acharya, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of 19b Fab Bound to HIV-1 Env 5768-p27 Peptide

Fetics, S., Acharya, P.

To be published.

Macromolecule Content

Total Structure Weight: 51.01 kDa
Atom Count: 3,670
Modeled Residue Count: 439
Deposited Residue Count: 472
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
19b Fab Light Chain	A	213	Homo sapiens	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
19b Fab Heavy Chain	B	216	Homo sapiens	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5768-p27 Envelope glycoprotein	C [auth D]	43	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for D2CJY3 (Human immunodeficiency virus type 1) Explore D2CJY3 Go to UniProtKB: D2CJY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2CJY3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.241 (Depositor), 0.240 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.951	α = 90
b = 87.176	β = 90
c = 131.677	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SAINT	data reduction
SADABS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-21

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-01-21
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.