5HJ3

Crystal structure of host-primed Ebola virus GP, GPcl.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Host-Primed Ebola Virus GP Exposes a Hydrophobic NPC1 Receptor-Binding Pocket, Revealing a Target for Broadly Neutralizing Antibodies.

Bornholdt, Z.A.Ndungo, E.Fusco, M.L.Bale, S.Flyak, A.I.Crowe, J.E.Chandran, K.Saphire, E.O.

(2016) Mbio 7: e02154-e02115


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
C, G, K, O
179Zaire ebolavirus (strain Mayinga-76)Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  Q05320
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
D, H, L, P
136Zaire ebolavirus (strain Kikwit-95)Gene Names: GP
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95))
Go to UniProtKB:  P87666
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
KZ52 Antibody Fragment
E, I, M, A
226N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
KZ52 Antibody Fragment
F, J, N, B
217N/AN/A
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, H, L, P
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 193.103α = 90.00
b = 193.103β = 90.00
c = 350.320γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-05-04
    Type: Database references