5CD5

Crystal structure of an immature VRC01-class antibody DRVIA7 from a Chinese donor bound to clade A/E HIV-1 gp120 core

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.396 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Key gp120 Glycans Pose Roadblocks to the Rapid Development of VRC01-Class Antibodies in an HIV-1-Infected Chinese Donor.

Kong, L., Ju, B., Chen, Y., He, L., Ren, L., Liu, J., Hong, K., Su, B., Wang, Z., Ozorowski, G., Ji, X., Hua, Y., Chen, Y., Deller, M.C., Hao, Y., Feng, Y., Garces, F., Wilson, R., Dai, K., O'Dell, S., McKee, K., Mascola, J.R., Ward, A.B., Wyatt, R.T., Li, Y., Wilson, I.A., Zhu, J., Shao, Y.

(2016) Immunity 44: 939-950


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
93TH057 HIV-1 gp120 core
A
353Human immunodeficiency virus 1Mutation(s): 0 
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus 1)
Go to UniProtKB:  A0A0M3KKW9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DRVIA7 Fab Heavy Chain
C
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DRVIA7 Fab Light Chain
D
210N/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 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.396 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.253 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.325α = 90.00
b = 72.325β = 90.00
c = 338.750γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2015-07-03 
  • Released Date: 2016-04-06 
  • Deposition Author(s): Kong, L., Wilson, I.A.

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2018-09-05
    Type: Data collection, Database references, Derived calculations