5BZD

Crystal Structure of PCDN-27A, an antibody from the PCDN family of HIV-1 antibodies

• PDB DOI: https://doi.org/10.2210/pdb5BZD/pdb

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


• Deposited: 2015-06-11 Released: 2016-05-25 
• Deposition Author(s): Garces, F., WILSON, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.247 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch

MacLead, D., Choi, N.M., Briney, B., Garces, F., Ver, L.S., Landais, E., Murrell, B., Wrin, T., Kilembe, W., Liang, C.-H., Ramos, A., Bian, C., Wickramasinghe, L., Kong, L., Eren, K., Wu, C.-Y., Wong, C.-H., The IAVI Protocol C Investigators & The IAVI African HIV Research Network, Pond, S.L.K., Wilson, I.A., Burton, D.R., Poignard, P.

(2016) Immunity 44: 1215-1226

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96.58 kDa 
• Atom Count: 6,733 
• Modelled Residue Count: 882 
• Deposited Residue Count: 892 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5G8 HIV Antibody light chain	A, C	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5G8 HIV Antibody heavy chain	B, D	232	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.247 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.861	α = 90
b = 120.375	β = 96.43
c = 111.098	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Garces, F., WILSON, I.A.

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Data collection
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description