4YDL

Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex with HIV-1 clade AE strain 93TH057gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.174

Literature

Macromolecules
Sequence Display for 4YDL

Classification: IMMUNE SYSTEM

Total Structure Weight: 179441.30

Macromolecule Entities
Molecule Chains Length Organism Details
Envelope glycoprotein gp160,Envelope glycoprotein gp160 A, G 353 Human immunodeficiency virus 1 Fragment: UNP residues 43-122, 201-303, 325-486
Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HEAVY CHAIN OF ANTIBODY C38-VRC18.02 B, H 226 Homo sapiens
LIGHT CHAIN OF ANTIBODY C38-VRC18.02 C, L 211 Homo sapiens

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

A, G 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, C, G, L N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

C, L SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
B, H L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.174
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 66.33 α = 90.00
b = 213.09 β = 90.17
c = 68.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-02-22
  • Released Date: 2015-06-03
  • Deposition author(s): Zhou, T., Srivatsan, S., Kwong, P.D.

Revision History

  • 2015-06-10
    Type: Database references
  • 2015-06-17
    Type: Database references