Primary Citation PubMed: 17301785
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Protective versus pathogenic anti-CD4 immunity: insights from the study of natural resistance to HIV infection.
(2009) J Transl Med 7
PubMed: 19943950 | PubMedCentral: PMC2789051 | DOI: 10.1186/1479-5876-7-101
C-alpha atoms B-factors were then extracted from the PDB files of the compared structures (accession numbers 3CD4 and 2NXY for CD4 and CD4-gp120 complex, respectively) as a measure of local backbone m... bility [ 71 ](Figure 2 ).
Data were calculated from PDB files 3CD4 and 2NXY for free and complexed CD4, respectively.
Publication Year: 2009
Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity.
(2010) Nat Struct Mol Biol 17
PubMed: 20357769 | PubMedCentral: PMC2949298 | DOI: 10.1038/nsmb.1796
We solved the structure by molecular replacement using Phaser 30 by searching for four components; V H -V L and C H 1-C L from the 21c Fab structure, the HXBc2 core plus CD4 D1 (PDB code 2NXY 7 , and ... D4 D2.
Publication Year: 2010
Structure-guided alterations of the gp41-directed HIV-1 broadly neutralizing antibody 2F5 reveal new properties regarding its neutralizing function.
(2012) PLoS Pathog 8
PubMed: 22829767 | PubMedCentral: PMC3400562 | DOI: 10.1371/journal.ppat.1002806
(B) Model of the HIV spike with gp120 (green) bound to the antibody 17b (orange), the primary virus receptor CD4 (yellow) (PDB:2NXY) and the MPER (modified from PDB:3G9R) (red [2F5 eptitope], blue [4E... 0 epitope] and yellow) bound to the antibody 2F5 (black) with the wt CDRH3 (magenta) positioned within the groove between two of the MPER helices.
Publication Year: 2012
CD4 binding determinant mimicry for HIV vaccine design.
(2012) Front Immunol 3
PubMed: 23251137 | PubMedCentral: PMC3523313 | DOI: 10.3389/fimmu.2012.00383
, CD4 liganded 1GC1, 1G9M, 1G9N, 1RZJ, 1RZK, 3JWD, 3JWO, 2NXY, 2NXZ, 2NY5, 2B4C, 2QAD; unliganded 2BF1, 3TGQ, 3TGR, 3TGT, 3TIH; CD4BD OD antibody liganded 3NGB, 3SE8, 3SE9, 3U7Y, 2NY7, 3HI1, 3IDX; low... molecular-weight CD4 mimetic liganded 1YYL, 1YYM, 2I5Y, 2I60, 3TGS).
Epitope mapping of M36, a human antibody domain with potent and broad HIV-1 inhibitory activity.
(2013) PLoS One 8
PubMed: 23776690 | PubMedCentral: PMC3679054 | DOI: 10.1371/journal.pone.0066638
For protein-ligand docking, 3D structure of gp120 (PDB code: 2NXY) was retrieved from the PDB  and initialized as receptor molecules with the DS 3.5 tool “Protein Preparation”.
M36 -binding interface on gp120 revealed by molecular docking To gain insights into the interaction of m36 with gp120, we docked the m36 model with a gp120 crystal structure (2NXY) using the ZDOCK program.
Publication Year: 2013
Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120.
(2013) Nat Struct Mol Biol 20
PubMed: 23708606 | PubMedCentral: PMC3823233 | DOI: 10.1038/nsmb.2594
For the quaternary complex, multiple components were used for phasing: 17b Fab (PDB ID: 2NXY), soluble CD4 (PDB ID: 2NXY), gp120 core (PDB ID: 2NXY) and high-resolution unliganded PGT 135 Fab as deter... ined here.
Strategic addition of an N-linked glycan to a monoclonal antibody improves its HIV-1-neutralizing activity.
(2013) Nat Biotechnol 31
PubMed: 24097413 | PubMedCentral: PMC3825789 | DOI: 10.1038/nbt.2677
The complex was modeled by superimposing the structure of D1 and D2 of CD4 in complex with gp120 (Protein Data Bank accession number 2NXY) onto the same domains of CD4 in complex with ibalizumab (PDB ... O2D).
To further explore the role of V5 glycosylation in ibalizumab susceptibility, we modeled the interactions between gp120, CD4 and ibalizumab using the structures reported to the Protein Data Bank (accession number 2NXY and 3O2D).
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