3SE9

Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with HIV-1 gp120

Structural Biology Knowledgebase: 3SE9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3SE9

Classification: VIRAL PROTEIN / IMMUNE SYSTEM

Total Structure Weight: 90841.89

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 Clade AE strain 93TH057 gp120 G 353 Human immunodeficiency virus 1 Fragment: Core gp120 with trancations
Gene Name(s): env
Heavy chain of antibody VRC-PG04 H 228 Homo sapiens Fragment: Antigen binding fragement of heavy chain
Light chain of antibody VRC-PG04 L 208 Homo sapiens Fragment: antibody light chain

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

G N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

H 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

G, L SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

G GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BU3
Query on BU3

G (R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

G, H, L CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.190
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.80 α = 90.00
b = 66.48 β = 90.00
c = 237.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-06-10
  • Released Date: 2011-08-10
  • Deposition author(s): Kwong, P.D., Zhou, T.

Revision History

  • 2011-10-05
    Type: Citation | Details: Citation update