3QEG | pdb_00003qeg

Crystal structure of human N12-i2 Fab, an ADCC and neutralizing anti-HIV-1 Env antibody

• PDB DOI: https://doi.org/10.2210/pdb3QEG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2011-01-20 Released: 2012-01-25 
• Deposition Author(s): Guan, Y., DeVico, A.L., Lewis, G.K., Pazgier, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.236 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human N12-i2 Fab, an ADCC and neutralizing anti-HIV-1 Env antibody

Guan, Y., DeVico, A.L., Lewis, G.K., Pazgier, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 49.09 kDa 
• Atom Count: 3,562 
• Modeled Residue Count: 429 
• Deposited Residue Count: 454 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment of human anti-HIV antibody N12-i2, heavy chain	A [auth H]	239	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment of human anti-HIV antibody N12-i2, light chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.236 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.906	α = 90
b = 78.906	β = 90
c = 315.147	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Guan, Y., DeVico, A.L., Lewis, G.K., Pazgier, M.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-27
  Changes: Structure summary