6DB6

Crystal structure of anti-HIV-1 V3 Fab 311-11D in complex with a HIV-1 gp120 V3 peptide from MN strain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.978 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Comparison of Human Anti-HIV-1 gp120 V3 Monoclonal Antibodies of the Same Gene Usage Induced by Vaccination and Chronic Infection.

Chan, K.W.Pan, R.Costa, M.Gorny, M.K.Wang, S.Lu, S.Kong, X.P.

(2018) J. Virol. 92: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Human monoclonal anti-HIV-1 gp120 V3 antibody 311-11D Fab heavy chain
H
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Human monoclonal anti-HIV-1 gp120 V3 antibody 311-11D Fab light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIV-1 gp120 V3 peptide from MN strain
P
23Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: env
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P05877
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
H
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
FCA
Query on FCA

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Download CCD File 
H
ALPHA-D-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-PHYPRBDBSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.978 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.568α = 90.00
b = 69.157β = 90.00
c = 141.887γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI100151
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI082676
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI082274
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI087191
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI112546

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references
  • Version 1.2: 2018-09-12
    Type: Data collection, Database references