6CE0

Crystal structure of a HIV-1 clade B tier-3 isolate H078.14 UFO-BG Env trimer in complex with broadly neutralizing Fabs PGT124 and 35O22 at 4.6 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.602 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.313 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

HIV-1 vaccine design through minimizing envelope metastability.

He, L.Kumar, S.Allen, J.D.Huang, D.Lin, X.Mann, C.J.Saye-Francisco, K.L.Copps, J.Sarkar, A.Blizard, G.S.Ozorowski, G.Sok, D.Crispin, M.Ward, A.B.Nemazee, D.Burton, D.R.Wilson, I.A.Zhu, J.

(2018) Sci Adv 4: eaau6769-eaau6769


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
B
140Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env, env
Find proteins for Q2N0T3 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0T3
Find proteins for Q2N0S5 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
G
487Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
Find proteins for A4ZPX1 (Human immunodeficiency virus 1)
Go to UniProtKB:  A4ZPX1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
35O22 Heavy chain
D
243N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
35O22 Light chain
E
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PGT124 Heavy chain
H
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PGT124 Light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
D, G, H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
D, G, H
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, D, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.602 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.313 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 127.351α = 90.00
b = 127.351β = 90.00
c = 316.350γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release