Primary Citation PubMed: 11188697
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Search for allosteric disulfide bonds in NMR structures.
(2007) BMC Struct Biol 7
PubMed: 17640393 | PubMedCentral: PMC1949407 | DOI: 10.1186/1472-6807-7-49
2 Eght X-ray structures from PDB IDs 1g9m , 1g9n , 1gcn , 1rzj , 1rzk , 1yy1 , 1yym and 2b4c were used for this analysis from.
Publication Year: 2007
The V1-V3 region of a brain-derived HIV-1 envelope glycoprotein determines macrophage tropism, low CD4 dependence, increased fusogenicity and altered sensitivity to entry inhibitors.
(2008) Retrovirology 5
PubMed: 18837996 | PubMedCentral: PMC2576352 | DOI: 10.1186/1742-4690-5-89
Unfortunately, the BR gp120 could not be modeled with any of the reported gp120 crystal structures, while the SPL gp120 did return a good model based on the HIV-1 YU-2 gp120 crystal structure (1G9N) [... 10 ].
Publication Year: 2008
Integrating T-cell epitope annotations with sequence and structural information using DAS.
(2008) Bioinformation 3
PubMed: 19238238 | PubMedCentral: PMC2639660 | DOI: null
SPICE"s alignment server automatically maps the protein sequence to a 3D structure (1G9N in this example).
RASMOT-3D PRO: a 3D motif search webserver.
(2009) Nucleic Acids Res 37
PubMed: 19417073 | PubMedCentral: PMC2703991 | DOI: 10.1093/nar/gkp304
CD4–gp120 complex coordinates were taken from PDB file 1g9n.
Publication Year: 2009
Broad-spectrum inhibition of HIV-1 by a monoclonal antibody directed against a gp120-induced epitope of CD4.
(2011) PLoS One 6
PubMed: 21818294 | PubMedCentral: PMC3139607 | DOI: 10.1371/journal.pone.0022081
Supporting Information Figure S1 Local conformation of the putative DB81 epitope in the unliganded (green; accession code: 1WIP/MMDB 6042) and gp120-bound (purple; accession code: 1G9N/MMDB 14984) tri... imensional structures of human CD4.
Publication Year: 2011
Systematic protein-protein docking and molecular dynamics studies of HIV-1 gp120 and CD4: insights for new drug development.
(2011) Daru 19
PubMed: 23008694 | PubMedCentral: PMC3436085 | DOI: null
1rzk and 1g9n are the only structures that do not expose unnatural binding distances due to missing amino acids.
Table 3 Root mean square deviations (RMSDs) of the docked conformations (1-10 for FireDock) for 1rzk and 1g9n protein complexes (directed and blind approaches) with reference to the minimized crystal structures as calculated by Swiss-PdbViewer.
Table 1 Root Mean Square Deviations (RMSDs) of the minimized structures with respect to the initial crystal structure for 1rzk and 1g9n protein complexes with their respective amino acid mutants as calculated by Swiss-PdbViewer.
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).
Publication Year: 2012
Structural plasticity and conformational transitions of HIV envelope glycoprotein gp120.
(2012) PLoS One 7
PubMed: 23300605 | PubMedCentral: PMC3531394 | DOI: 10.1371/journal.pone.0052170
Experimental B-factors are from the crystal structure (PDB ID: 1G9N)  ; theoretical values derive from the mean-squared fluctuations, <| r – r 0 | 2 >, as summed from all m... des from an isotropic ENM calculation from the entire gp120:D1:V H V L complex, noting that B = 8π 2 <| r – r 0 | 2 >/3.
ENM-generated atomic mobility factors correlate with experimental values In order to test the validity of the ENM calculations, we compare the ENM generated atomic mobility factors (B-factors) of gp120 complex with those experimentally observed in gp120 crystal structure (pdb ID: 1G9N, YU2 strain)  .
( A–C ) Comparisons of gp120 structures in ( A ) the CD4-bound state (PDB ID: 1G9N)  , ( B ) the b12 antibody-bound state (PDB ID: 2NY7)  , and ( C ) the F105 antibody-bound state (PDB ID: 3HI1)  .
Methods Protein Structures The crystal structure of gp120 core from the YU2 primary isolate in complex with a two- domain fragment of CD4 and the antigen-binding fragment of a human antibody at 2.9 Å resolution (pdb id: 1G9N) was used for the ENM and NMA calculations.
( D–E ) Comparisons of complexes between gp120 and various protein ligands: gp120 with ( D ) CD4 (PDB ID: 1G9N)  .
The structure of loop LV4 for the CD4-bound state was modeled by first patching in loop LV4 from the YU2 gp120 structure (PDB ID = 1G9N) and then by refining the resulting structure using the MODELLER software.
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