6OZ3

Crystal structure of broadly neutralizing antibody N49P9.1 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core

• PDB DOI: https://doi.org/10.2210/pdb6OZ3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2019-05-15 Released: 2020-08-19 
• Deposition Author(s): Tolbert, W.D., Pazgier, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.295 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 

Starting Models: experimental

Literature

Crystal structure of broadly neutralizing antibody N49P9.1 Fab in complex with HIV-1 Clade A/E strain 93TH)57 gp120 core

Tolbert, W.D., Pazgier, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 87.67 kDa 
• Atom Count: 5,817 
• Modelled Residue Count: 733 
• Deposited Residue Count: 779 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
clade A/E 93TH057 HIV-1 gp120 core	A [auth G]	355	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: HIV-1 Env
UniProt
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus 1) Explore A0A0M3KKW9  Go to UniProtKB:  A0A0M3KKW9
Glycosylation
Glycosylation Sites: 11

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N49P9.1 antibody Fab heavy chain	B [auth H]	221	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N49P9.1 antibody Fab light chain	C [auth L]	203	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G], N [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	O [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.295 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.754	α = 90
b = 110.454	β = 90
c = 152.165	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Tolbert, W.D., Pazgier, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI116274
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI120756
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI129769

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary