5T4Z

STRUCTURE OF THE ANTI-HIV ANTIBODY DH501 THAT BINDS GP120 V3 GLYCAN AND THE BASE OF V3 WITH FREE MAN9 GLYCAN

• PDB DOI: https://doi.org/10.2210/pdb5T4Z/pdb

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


• Deposited: 2016-08-30 Released: 2017-03-08 
• Deposition Author(s): Nicely, N.I., Haynes, B.F.
• 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: 1.99 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

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)

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: 95.58 kDa 
• Atom Count: 6,898 
• Modelled Residue Count: 868 
• Deposited Residue Count: 892 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody DH501 Fab heavy chain	A [auth H], C [auth A]	230	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody DH501 Fab light chain	B [auth L], D [auth B]	216	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	E [auth C]	3		N/A
Glycosylation Resources
GlyTouCan:  G57891XD GlyCosmos:  G57891XD GlyGen:  G57891XD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	F [auth H], G [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.757	α = 90
b = 115.997	β = 97.39
c = 76.889	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: 2017-03-08 
Deposition Author(s): Nicely, N.I., Haynes, B.F.

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

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 1.1: 2017-03-15
  Changes: Structure summary
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary