6MFT

Crystal structure of glycosylated 426c HIV-1 gp120 core G459C in complex with glVRC01 A60C heavy chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.315 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core.

Borst, A.J.Weidle, C.E.Gray, M.D.Frenz, B.Snijder, J.Joyce, M.G.Georgiev, I.S.Stewart-Jones, G.B.Kwong, P.D.McGuire, A.T.DiMaio, F.Stamatatos, L.Pancera, M.Veesler, D.

(2018) Elife 7: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heavy Chain glVRC01
H, A
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Light chain glVRC01
L, B
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Gp120
G, C
347N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

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Download CCD File 
C
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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C, G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
C, G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
G
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
C, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, H
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.315 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 197.082α = 90.00
b = 109.003β = 114.47
c = 103.225γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesAI081625

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references