Citations in PubMed

Primary Citation PubMed: 9108481 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 12

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Anti-HIV-1 activity of cellulose acetate phthalate: synergy with soluble CD4 and induction of "dead-end" gp41 six-helix bundles.

(2002) BMC Infect Dis 2

PubMed: 11983022 | PubMedCentral: PMC113252 | DOI: null

The docking simulations of CTAP were performed using the DockVision program [ 30 ] on the entire surface of the gp41 core structure {The X-ray crystal structure of the gp41 core, 1aik, was retrieved f... om the protein databank }.

Publication Year: 2002

Dilation of the human immunodeficiency virus-1 envelope glycoprotein fusion pore revealed by the inhibitory action of a synthetic peptide from gp41.

(1998) J Cell Biol 140

PubMed: 9442107 | PubMedCentral: PMC2132584 | DOI: null

The protein models shown in b , c , e , and f were developed from a recently determined crystal structure of gp41 fragments in the heterotrimeric coiled-coil conformation ( 10 ) (1AIK.

Publication Year: 1998

Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus.

(2009) PLoS Pathog 5

PubMed: 19424420 | PubMedCentral: PMC2671596 | DOI: 10.1371/journal.ppat.1000418

Schema analysis PDB files detailing the three dimensional structures of both gp120 (PDB ID: 2B4C, determined by X-ray diffraction, resolution of 3.3 Å, 338 amino acids, [55] ),... and gp41 (PDB ID 1AIK, determined by X-ray diffraction, resolution of 2 Å, 70 amino acids, [56] ) were obtained from .

Publication Year: 2009

Crystal structure of HIV-1 gp41 including both fusion peptide and membrane proximal external regions.

(2010) PLoS Pathog 6

PubMed: 20463810 | PubMedCentral: PMC2865522 | DOI: 10.1371/journal.ppat.1000880

The structure was solved by molecular replacement using the program Phaser [53] and the model of the gp41 core (PDB ID: 1AIK) by applying the twin law of h, -h-k, -l on the data, revea... ing 3 molecules in the asymmetric unit.

Publication Year: 2010

Structural basis of HIV-1 neutralization by affinity matured Fabs directed against the internal trimeric coiled-coil of gp41.

(2010) PLoS Pathog 6

PubMed: 21085615 | PubMedCentral: PMC2978731 | DOI: 10.1371/journal.ppat.1001182

Three sets of tryptophan side chains seen in 6-HB gp41 trimers, two X-ray structure, pdb codes 1AIK [7] and 1ENV [8] , and one NMR structure, pdb code 1QCE [10&... x0005d; , [52] , are shown in white, blue and red sticks, respectively.

Several residues, such as Trp-628 , Trp-631 and Ile-635 on the C -HR helix and Ile-573 and Val-570 ( Ile-208 and Val-205 in the Fab 8066 and 8062 complexes, respectively) on the N -HR helix from the same molecule of gp41, maintain numerous intramolecular hydrophobic interactions (numbering for the Cc residues is taken from the 1AIK structure [7] and corresponds to the numbering of the native gp160 sequence).

Publication Year: 2010

Distinct conformational states of HIV-1 gp41 are recognized by neutralizing and non-neutralizing antibodies.

(2010) Nat Struct Mol Biol 17

PubMed: 21076402 | PubMedCentral: PMC2997185 | DOI: 10.1038/nsmb.1950

The structure was determined by molecular replacement using HIV-1 gp41 monomer (pdb:1AIK; ref 10 ) and a library of Fab coordinates as search models 37 .

Publication Year: 2010

Structural mechanism of trimeric HIV-1 envelope glycoprotein activation.

(2012) PLoS Pathog 8

PubMed: 22807678 | PubMedCentral: PMC3395603 | DOI: 10.1371/journal.ppat.1002797

By fitting coordinates for the N-terminal gp41 helix (N34; PDB ID: 1AIK) into the density map, we arrive at an assignment in which the fusion peptide is at the free end facing the target cell membrane... and is connected to the rest of the polypeptide at the bottom on the side of the viral membrane.

One copy of the gp41 N-terminal helix (cyan) of 1AIK coordinates (N34) was fitted individually into each of the three densities, which occupy the central region of the spike that is essentially a cavity in the unliganded state.

(b) Top view of the locations of the same helices in the crystal structure (1AIK) of the six-helix bundle formed by the three N- and three C-terminal helices, illustrating the more compact packing in the post-fusion state.

Publication Year: 2012

Computer-Aided Approaches for Targeting HIVgp41.

(2012) Biology (Basel) 1

PubMed: 23730525 | PubMedCentral: PMC3666032 | DOI: 10.3390/biology1020311

To illustrate this point, we aligned five gp41 structures from the PDB (1AIK, 2KP8, 2Q5U, 2ZFC, and 3O3X) along the backbone α-carbons.

NHR/CHR Peptide Mixtures Example Structure (PDB 1AIK): Summary of PDB Structures: 1 N36/C34: 1AIK [ 38 ].

Figure 4 ( A ) Docked pose of compound SB-D04 (blue) [ 69 ] in PDB structure 1AIK (gray).

Therefore, in the absence of a fully-flexibly receptor model during docking or virtual screening, it may be most appropriate to use a structure of a bound NHR trimer with the ligand removed (e.g., 1AIK with a CHR peptide removed).

The structure 1AIK contains CHR-derived peptides, and the structure 2KP8 contains an NMR model of a small molecule bound, both of which were removed.

Publication Year: 2012

Design of Small Molecules with HIV Fusion Inhibitory Property Based on Gp41 Interaction Assay.

(2013) Avicenna J Med Biotechnol 5

PubMed: 23799176 | PubMedCentral: PMC3689560 | DOI: null

Crystallographic structures of Gp41 (PDB ID: 1F23 and 1AIK) were taken from PDB (Protein Data Bank) [ ] and used as a target in docking process ( 2 ) .

Publication Year: 2013

Complexes of neutralizing and non-neutralizing affinity matured Fabs with a mimetic of the internal trimeric coiled-coil of HIV-1 gp41.

(2013) PLoS One 8

PubMed: 24244293 | PubMedCentral: PMC3820714 | DOI: 10.1371/journal.pone.0078187

For comparisons of the trimers of N-HR helices we have also used, in addition to the structures presented here, the structures of the same antibodies complexed to 5-Helix (3MA9 and 3MAC), as well as t... e crystal structure of the six-helix bundle (6-HB) of gp41 ( [24] ; PDB code 1AIK).

(A) N-HR helices of the (Fab 8066) 3 /3-H complex (red), of the (Fab 8062) 3 /3-H complex (blue), of the 6-helix bundle of gp41 with a GCN4 zipper [25] : PDB code 1ENV (green), and of the 6-helix bundle of gp41 [24] ; PDB code 1AIK (orange).

Publication Year: 2013

Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking: anchors modified polyanions interference with the HIV-1 fusion mediator.

(2014) J Comput Aided Mol Des 28

PubMed: 24862639 | PubMedCentral: PMC4050303 | DOI: 10.1007/s10822-014-9749-8

PDB 1AIK HIV gp41 core structure.

doi:10.2210/pdb1aik/pdb 24.

The same viral target model, based on 1AIK PDB [ 23 ] in application to the trimeric complex [HR1] 3 , was used for the MD simulation as the starting target’s 3D-conformation.

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4348022

Several postfusion gp41 structures have been determined ranging from a minimal, protease-treated, crystal structure (residues 556 gp41 -581 gp41 ; 628 gp41 -661 gp41 ; PDB ID: 1AIK 8 ) with 80% sequen... e identity to BG505 46 to a more complete gp41 structure (residues 531 gp41 -581 gp41 ; 624-681 gp41 ; PDB ID: 2X7R 24 ) and an NMR structure that includes the cysteine loop (residues 539 gp41 -665 gp41 ; PDB ID: 2EZO 25 ) of the simian immunodeficiency virus (SIV), which shares 48% sequence identity with BG505 46 and is substantially similar to the HIV-1 structures (less than 1-Å Cα rmsd between overlapping residues of 1AIK and 2EZO).

Publication Year: 2014