3TGS

Crystal structure of HIV-1 clade C strain C1086 gp120 core in complex with NBD-556

• PDB DOI: https://doi.org/10.2210/pdb3TGS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2011-08-17 Released: 2012-04-04 
• Deposition Author(s): Kwon, Y.D., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.295 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global 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: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 83.06 kDa 
• Atom Count: 5,742 
• Modelled Residue Count: 690 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 clade C1086 gp120 core	A, B	358	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for C6G099 (Human immunodeficiency virus 1) Explore C6G099  Go to UniProtKB:  C6G099

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
03G	I [auth A], M [auth B]	N-(4-chlorophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide C17 H24 Cl N3 O2 ZKXLQCIOURANAD-UHFFFAOYSA-N
NAG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth A], K [auth A], L [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
03G	PDBBind:  3TGS	Kd: 4100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.295 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.96	α = 90
b = 126	β = 90
c = 191.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Kwon, Y.D., Kwong, P.D.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2014-12-17
  Changes: Non-polymer description
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary