6MU8

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-386150 in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.993 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry.

Lai, Y.T.Wang, T.O'Dell, S.Louder, M.K.Schon, A.Cheung, C.S.F.Chuang, G.Y.Druz, A.Lin, B.McKee, K.Peng, D.Yang, Y.Zhang, B.Herschhorn, A.Sodroski, J.Bailer, R.T.Doria-Rose, N.A.Mascola, J.R.Langley, D.R.Kwong, P.D.

(2019) Nat Commun 10: 47-47


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
B
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
35O22 scFv heavy chain portion
D
134N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
35O22 scFv light chain portion
E
114N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
G
481Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
3H109L Fab heavy chain
H
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
3H109L Fab light chain
L
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

Download SDF File 
Download CCD File 
G
1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-1,2-dione
C21 H17 Br F N3 O3
FHPUNKHJTFLQMK-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.993 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 131.410α = 90.00
b = 131.410β = 90.00
c = 315.470γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release