3RJQ

Crystal structure of anti-HIV llama VHH antibody A12 in complex with C186 gp120

• PDB DOI: https://doi.org/10.2210/pdb3RJQ/pdb

• Classification: Viral Protein/Immune system
• Organism(s): HIV-1 M:B_HXB2R, Lama glama
• Mutation(s): No 


• Deposited: 2011-04-15 Released: 2012-05-02 
• Deposition Author(s): Chen, L., McLellan, J.S., Kwon, Y.D., Schmidt, S., Wu, X., Zhou, T., Yang, Y., Zhang, B., Forsman, A., Weiss, R.A., Verrips, T., Mascola, J., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.299 
• R-Value Work: 0.255 
• R-Value Observed: 0.257 

Literature

Crystal structure of anti-HIV A12 VHH of llama antibody in complex with C1086 gp120

Chen, L., McLellan, J.S., Kwon, Y.D., Schmidt, S., Wu, X., Zhou, T., Yang, Y., Zhang, B., Forsman, A., Weiss, R.A., Verrips, T., Mascola, J., Kwong, P.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 59.98 kDa 
• Atom Count: 3,390 
• Modelled Residue Count: 419 
• Deposited Residue Count: 525 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C186 gp120	A	382	HIV-1 M:B_HXB2R	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Llama VHH A12	B	143	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.299 
• R-Value Work: 0.255 
• R-Value Observed: 0.257 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.6	α = 90
b = 66.6	β = 90
c = 266.92	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Chen, L., McLellan, J.S., Kwon, Y.D., Schmidt, S., Wu, X., Zhou, T., Yang, Y., Zhang, B., Forsman, A., Weiss, R.A., Verrips, T., Mascola, J., Kwong, P.D.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2012-06-13
  Changes: Database references
• Version 1.2: 2012-09-12
  Changes: Structure summary
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary