4R4F

Crystal structure of non-neutralizing, A32-like antibody 2.2c in complex with HIV-1 YU2 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.514 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection.

Acharya, P.Tolbert, W.D.Gohain, N.Wu, X.Yu, L.Liu, T.Huang, W.Huang, C.C.Kwon, Y.D.Louder, R.K.Luongo, T.S.McLellan, J.S.Pancera, M.Yang, Y.Zhang, B.Flinko, R.Foulke, J.S.Sajadi, M.M.Kamin-Lewis, R.Robinson, J.E.Martin, L.Kwong, P.D.Guan, Y.DeVico, A.L.Lewis, G.K.Pazgier, M.

(2014) J.Virol. 88: 12895-12906


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Env gp120
A
376Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: env
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P35961
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody 2.2c LIGHT CHAIN
L
209N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antibody 2.2c heavy CHAIN
H
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
M48U1 peptide
R
28N/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
BU3
Query on BU3

Download SDF File 
Download CCD File 
A, L
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001094
Query on PRD_001094
RCD4-MIMETIC MINIPROTEIN M48U1Peptide-like / Inhibitor

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OAS
Query on OAS
L
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.514 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 158.321α = 90.00
b = 171.230β = 90.00
c = 227.974γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Structure summary
  • Version 1.2: 2014-10-22
    Type: Database references
  • Version 1.3: 2018-01-31
    Type: Experimental preparation