5F4U

HIV-1 gp120 complex with BNM-IV-197

• PDB DOI: https://doi.org/10.2210/pdb5F4U/pdb

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


• Deposited: 2015-12-03 Released: 2016-03-30 
• Deposition Author(s): Liang, S., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.280 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 81.45 kDa 
• Atom Count: 5,520 
• Modelled Residue Count: 671 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C	A, B	350	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
5VH	I [auth A], Q [auth B]	~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide C22 H26 Cl F N8 O2 SEZMROBQXWBHMW-FZKQIMNGSA-N
NAG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.280 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.439	α = 90
b = 128.123	β = 90
c = 193.599	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Liang, S., Hendrickson, W.A.

Revision History  

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary