Primary Citation PubMed: 9641677
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MIMOX: a web tool for phage display based epitope mapping.
(2006) BMC Bioinformatics 7
PubMed: 17038191 | PubMedCentral: PMC1618411 | DOI: 10.1186/1471-2105-7-451
The structure of HIV gp120 envelope glycoprotein in complex with 17b has been solved [PDB: 1GC1] and 17b epitope has been recorded in the CED database as CE0058, which is composed of CK(119,121) + VTQ... C(200,202–205) + RKQI(419,421–423) + KMYP (432,434,435,437).
Publication Year: 2006
Spatial chemical conservation of hot spot interactions in protein-protein complexes.
(2007) BMC Biol 5
PubMed: 17925020 | PubMedCentral: PMC2231411 | DOI: 10.1186/1741-7007-5-43
Sens. 1a4y:A RNase inhibitor Angiogenin 4 0.74 0.78 0.75 0.18 0.78 0 0.75 0.8 14 1brs:A Barnase Barstar 6 0.75 1 0.5 n/a n/a n/a 0.5 0.67 8 1brs:D Barstar Barnase 6 1 1 1 n/a n/a n/a 1 1 6 1cbw I BPTI... Trypsin 7 1 0.88 1 0.75 0.62 1 0.75 1 9 1gc1:C CD4 gp120 6 0.74 0.86 0.67 0.58 0.62 0.67 0.81 0.33 49 1bxi:A Im9 E9 DNase 6 0.72 1 0.44 0.72 0.88 0.56 0.88 0.44 28 1dan:L Factor VII Tissue Factor 6 1 0.73 1 0.23 0.64 0 0.73 1 107 1jck:A TCR Vb SEC3 6 0.65 0.88 0.4 0.41 0.75 0 1 0.5 24 1jck:B SEC3 TCR Vb 6 0.75 1 0.5 0.31 0.5 0.12 1 0.62 10 1vfb:C HEL D.1.3 7 0.51 0.62 0.5 0.27 0.62 0.25 1 0 12 3hfm:Y HEL HYHEL 8 0.62 0.6 0.67 0.78 0.7 0.67 0.8 1 13 3hhr:A hGH hGHbp 4 0.74 1 0.52 0.59 0.44 0.68 0.94 0.32 161 Mean MAPPIS Mean Consurf Mean Robetta Total 6 0.77 0.86 0.66 0.48 0.66 0.4 0.85 0.64 440 (116) We compared the predictive power of MAPPIS with our previously developed multiple alignment methods.
Publication Year: 2007
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.
(2008) PLoS Comput Biol 4
PubMed: 18989394 | PubMedCentral: PMC2566816 | DOI: 10.1371/journal.pcbi.1000214
Thus, the following structures were used: Gag derived proteins: matrix p17, capsid p24, nucleocapsid p7 (PDB IDs: 1tam, 1e6j, 1a1t, respectively); Pol derived proteins: protease p10, reverse transcrip... ase p51, RNase p15, integrase p31 (PDB IDs: 1aaq, 1rtd, 1o1w, 2itg, respectively); Vpr p12/p10 (PDB ID: 1m8l); Tat p16/p14 (PDB ID: 1mnb); Rev p19 (PDB ID: 1etf); Vpu p16 (PDB ID: 1vpu); Env derived proteins: gp120, gp41 (PDB IDs: 1gc1, 1env, respectively); Nef p27/p25 (PDB ID: 2nef).
Publication Year: 2008
Identification of hot-spot residues in protein-protein interactions by computational docking.
(2008) BMC Bioinformatics 9
PubMed: 18939967 | PubMedCentral: PMC2579439 | DOI: 10.1186/1471-2105-9-447
Table 1 Initial dataset of complexes used in this work Complex a Res b Receptor Ligand Unbound receptor Res b Unbound ligand Res b Complex type c 1A22 2.60 Growth hormone receptor Growth hormone - - 1... GU 2.50 B/U 1A4Y 2.00 Ribonuclease inhibitor Angiogenin - - 1UN3 1.70 B/U 1AHW 3.00 Fab 5G9 Tissue Factor 1K6Q 2.40 2HFT 1.69 U/U 1AIE 1.50 p53 p53 - - - - B/B 1BRS 2.00 Barnase Barstar 1A2P 1.50 - - U/B 1BXI 2.05 Colicin E9 Immunity protein Im9 1FSJ 1.80 - - U/B 1DAN 2.00 Tissue Factor Factor VII 2HFT 1.69 - - U/B 1DFJ 2.30 Ribonuclease A Ribonuclease inhibitor 1FS3 1.40 2BNH 2.30 U/U 1DN2 2.70 IgG1 Fc fragment DCAWHLGELV WCT-NH 2 1H3V 3.10 - - U/B 3HFM 3.00 HYHEL-10 HEL 1GPO 1.95 3LZT 0.92 U/U 1GC1 2.50 CD4 gp120 1CDJ 2.50 - - U/B 1F47 1.95 Zipa FTSZ fragment 1F7W NMR - - U/B 1FC2 2.80 Fc fragment Protein A - - - - B/B 1FCC 3.50 Fc fragment Protein G 1H3V 3.10 - - U/B 1IAR 2.60 IL-4 receptor IL-4 - - 1HIK 2.60 B/U 1JCK 3.50 T-cell antigen receptor SEC3 1BEC 1.70 1CK1 2.60 U/U 1JRH 2.80 Antibody A6 Interferon-γ receptor - - - - B/B 1JTD 2.30 TEM-1 β-lactamase BLIP 1ZG4 1.55 - - U/B 1NMB 2.50 NC10 Neuraminidase N9 - - 7NN9 2.00 B/U 2PTC 1.90 Trypsin BPTI 1S0Q 1.02 1G6X 0.86 U/U 1VFB 1.80 Antibody D1.3 HEL - - 3LZT 0.92 B/U a PDB Code, b Resolution in Å; c B, Bound; U, Unbound For most of the complexes, the structure of only one of the two partners is available in the unbound conformation.
'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces.
(2009) Bioinformatics 25
PubMed: 19179356 | PubMedCentral: PMC2654803 | DOI: 10.1093/bioinformatics/btp058
However, only 13 of them are matched with PDB entries: 1a4y, 1ahw, 1brs, 1bxi, 1cbw, 1dan, 1dvf, 1gc1, 1jck, 1vfb, 2ptc, 2hfm and 3hhr.
Numbers of very warm and hot residues of the 13 protein complexes stored in ASEdb in comparison to those contained in our biclique patterns PDB ΔΔ G ≥1.5 kcal/mol ΔΔ G ≥2.0 kcal/mol ASEdb Biclique ASEdb Biclique 1A4Y 4 4 3 3 1AHW 1 1 1 1 1BRS 10 9 9 8 1BXI 7 7 6 6 1CBW 1 1 1 1 1DAN 6 6 3 3 1DVF 19 18 8 8 1GC1 1 0 0 0 1JCK 6 5 4 4 1VFB 6 5 3 3 2PTC 1 1 1 1 3HFM 6 5 5 4 3HHR 14 11 8 7 Total 82 73 52 49 sensitivity 73/82=89% 49/52=94% The larger ΔΔ G the residues are, more likely those are in our biclique patterns.
Publication Year: 2009
A feature-based approach to modeling protein-protein interaction hot spots.
(2009) Nucleic Acids Res 37
PubMed: 19273533 | PubMedCentral: PMC2677884 | DOI: 10.1093/nar/gkp132
The 17 protein–protein complexes analyzed PDB id First molecule Second molecule 1a4y RNase inhibitor Angiogenin 1a22 Human growth hormone Human growth hormone binding protein 1ahw Immunoglobul... n Fab5G9 Tissue factor 1brs Barnase Barstar 1bxi Colicin E9 Immunity Im9 Colicin E9 DNase 1cbw BPTI Trypsin inhibitor Chymotrypsin 1dan Blood coagulation factor VIIA Tissue factor 1dvf Idiotopic antibody FV D1.3 Anti-idiotopic antibody FV E5.2 1f47 Cell division protein ZIPA Cell division protein FTSZ 1fc2 Fc fragment Fragment B of protein A 1fcc Fc (IGG1) Protein G 1gc1 Envelope protein GP120 CD4 1jrh Antibody A6 Interferon-gamma receptor 1nmb N9 Neuramidase Fab NC10 1vfb Mouse monoclonal antibody D1.3 Hen egg lysozyme 2ptc BPTI Trypsin 3hfm Hen Egg Lysozyme lg FAB fragment HyHEL-10 An independent test set An independent test set is constructed from the BID ( 35 ) to further validate our SVM model.
Structural comparison between the unbound and bound states for various proteins using combinatorial extension Bound state a Unbound state b RMSD(Å) c Seq. PDB id Chain id PDB id Chain id identity (%) Angiogenin 1a4y B 1un3 A 0.76 99.1 hGH 1a22 A 1hgu – d 2.68 68.4 Tissue factor e 1ahw C 1tfh A 1.39 100.0 Barnase 1brs A 1bnf A 1.12 98.1 Barstar 1brs D 1a19 A 0.44 98.9 BPTI 1cbw D 1bpt – d 0.39 98.2 Tissue factor e 1dan T 1tfh A 0.63 100.0 RNase inhibitor 1dfj I 2bnh – d 1.50 100.0 CD4 1gc1 C 1cdj A 1.09 100.0 Hen egg lysozyme e 1vfb C 1lyz – d 1.11 100.0 Trypsin 2ptc I 1bpt – d 0.36 98.2 Lysozyme e 3hfm Y 1lyz – d 0.67 100.0 a A protein is in the bound state.
PTools: an opensource molecular docking library.
(2009) BMC Struct Biol 9
PubMed: 19409097 | PubMedCentral: PMC2685806 | DOI: 10.1186/1472-6807-9-27
pdb"); The equivalent Python code is: prot = Rigidbody(" 1GC1 .
In the following example in C++ the 1GC1 .
Rigidbody prot(" 1GC1 .
Immunoglobulin superfamily virus receptors and the evolution of adaptive immunity.
(2009) PLoS Pathog 5
PubMed: 19956667 | PubMedCentral: PMC2777377 | DOI: 10.1371/journal.ppat.1000481
(C–E) Ribbon drawings of the complexed D1 domains of (C) CD4 (  ; 1GC1), (D) hJAM-A (  ; 3EOY), and (E) CAR (  ; 1KAC).
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.
(2010) BMC Bioinformatics 11
PubMed: 20377884 | PubMedCentral: PMC2874803 | DOI: 10.1186/1471-2105-11-174
Table 1 Training set of protein structures PDB First molecule Second molecule 1a4y Angiogenin Ribonuclease Inhibitor 1a22 Human growth hormone Human growth hormone binding protein 1ahw Immunoglobulin ... ab 5G9 Tissue factor 1brs Barnase Barstar 1bxi Colicin E9 Immunity Im9 Colicin E9 DNase 1cbw BPTI Trypsin inhibitor Chymotrypsin 1dan Blood coagulation factor VIIA Tissue factor 1dvf Idiotopic antibody FV D1.3 Anti-idiotopic antibody FV E5.2 1fc2 Fc fragment Fragment B of protein A 1fcc Fc (IGG1) Protein G 1gc1 Envelope protein GP120 CD4 1jrh Antibody A6 Interferon-gamma receptor 1vfb Mouse monoclonal antibody D1.3 Hen egg lysozyme 2ptc BPTI Trypsin 3hfm Hen Egg Lysozyme lg FAB fragment HyHEL-10 Independent test set An independent test set was extracted from the BID database [ 11 ] to further assess the performance of our proposed method.
Publication Year: 2010
Palmitic acid analogs exhibit nanomolar binding affinity for the HIV-1 CD4 receptor and nanomolar inhibition of gp120-to-CD4 fusion.
(2010) PLoS One 5
PubMed: 20730055 | PubMedCentral: PMC2921400 | DOI: 10.1371/journal.pone.0012168
B ) Crystal structure of gp120-CD4 (PDB code 1GC1).
Results PA and gp120 binding sites on CD4 overlap To gain structural insights into the mechanisms of PA binding to the CD4 receptor, we used in silico molecular docking based on the known X-ray structure of the two N-terminal domains of CD4 (aa 26-206) (PDB code 1GC1) and a flexible PA ligand ( Figure 1 ).
The geometry of PA-CD4 with a highest score is shown in Figure 1A , and crystal structure of gp120-CD4 (PDB code 1GC1) binding is shown in Figure 1B .
A ) Molecular docking software Autodock 4.0 was used for blind docking of flexible PA onto rigid two N-terminal domains of CD4 (PDB code 1GC1).
Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure.
(2010) PLoS Pathog 6
PubMed: 21203482 | PubMedCentral: PMC3009598 | DOI: 10.1371/journal.ppat.1001249
The three possible sets of atomic coordinates that are available as starting points to carry out the automated fitting are the structure reported for unliganded SIV gp120 core (2BF1), the structure of... HIV-1 gp120 from the complex with b12 (2NY7), or the structure of HIV-1 gp120 from the complex with sCD4/17b (1GC1).
The gp120 coordinates (1GC1) are shown as red ribbons and were fitted using automated procedures into the density maps.
(a, b) Perspective views of gp120 monomer coordinates (1GC1) fit into the Env density maps obtained from SIVmneE11S (a) and SIVmac239 (b) using automated procedures.
(d) Automated fit of HIV-1 gp120 monomer coordinates (1GC1) into the density map with the CD4 binding site and the base of the V3 loop highlighted in yellow and green, respectively.
Novel peptides based on HIV-1 gp120 sequence with homology to chemokines inhibit HIV infection in cell culture.
(2011) PLoS One 6
PubMed: 21264298 | PubMedCentral: PMC3019152 | DOI: 10.1371/journal.pone.0014474
g007 Figure 7 Comparison of the structures of the fragments of gp120 (HIV HXB2 residues 331–344, PDB code 1gc1) and CCL4 (residues 47–64, PDB code 1hum).
Publication Year: 2011
Siglecs facilitate HIV-1 infection of macrophages through adhesion with viral sialic acids.
PubMed: 21931755 | PubMedCentral: PMC3169630 | DOI: 10.1371/journal.pone.0024559
The V1 and V2 loops are drawn in the figure, as both loops are missing in the crystal structure of the gp120 and CD4 complex (pdb code 1GC1).
Structural mechanism of trimeric HIV-1 envelope glycoprotein activation.
(2012) PLoS Pathog 8
PubMed: 22807678 | PubMedCentral: PMC3395603 | DOI: 10.1371/journal.ppat.1002797
(a, b) Two orthogonal views of the superposition of gp120 polypeptides derived from the complex with sCD4 and 17b (PDB ID: 1GC1) and the complex with VRC01 (PDB ID: 3NGB).
X-ray coordinates for the gp120-VRC01 complex (PDB ID:3NGB) were fitted into the map and subsequently aligned to the gp120-CD4/17b (PDB ID:1GC1) complex.
Maps in all panels were fitted with subsets of the X-ray coordinates from the gp120-sCD4/17b complex (PDB ID:1GC1).
Coordinates (PDB IDs: 3DNN, 3NGB, 3SE8, 2NY7 & 1GC1) were fitted into density maps using the software package UCSF Chimera  .
The gp120 chain and sCD4 chains from the 1GC1 structure are shown in red, and yellow, respectively, while the gp120 and VRC01 chains from the 3NGB structure are shown in magenta and green, respectively.
The map was fitted with three copies of the X-ray structures for the gp120-17b portion of the 1GC1 coordinates with gp120 (red) and 17b Fv fragments (light chain: yellow, heavy chain: green).
The map was fitted with three copies of the X-ray structures for the gp120-17b portion of the 1GC1 coordinates with color scheme as in Figure 9 .
Publication Year: 2012
A semi-supervised boosting SVM for predicting hot spots at protein-protein interfaces.
(2012) BMC Syst Biol 6 Suppl 2
PubMed: 23282146 | PubMedCentral: PMC3521187 | DOI: 10.1186/1752-0509-6-S2-S6
PDB 1st Molecule 2nd Molecule H NH 1a4y Angiogenin Ribonuclease Inhibitor 3 12 1a22 Human growth hormone Human growth hormone binding protein 7 29 1ahw Immunoglobulin Fab 5G9 Tissue factor 1 3 1brs Ba... nase Barstar 8 1 1bxi Colicin E9 Immunity Im9 Colicin E9 DNase 6 3 1cbw BPTI Trypsin inhibitor Chymotrypsin 1 4 1dan Blood coagulation factor VIIA Tissue factor 2 9 1dvf Idiotopic antibody FV D1.3 Anti-idiotopic antibody FV E5.2 6 1 1fc2 Fc fragment Fragment B of protein A 1 0 1fcc Fc (IGG1) Protein G 4 2 1gc1 Envelope protein GP120 CD4 0 11 1jrh Antibody A6 Interferon-gamma receptor 8 5 1vfb Mouse monoclonal antibody D1.3 Hen egg lysozyme 3 6 2ptc BPTI Trypsin 1 0 3hfm Hen Egg Lysozyme lg FAB fragment HyHEL-10 11 6 H stands for Hot Spot and NH stands for Non-Hot Spot .
CD4 binding determinant mimicry for HIV vaccine design.
(2012) Front Immunol 3
PubMed: 23251137 | PubMedCentral: PMC3523313 | DOI: 10.3389/fimmu.2012.00383
Created with PDB data 1GC1.
, 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).
(A) Superimposed CD4BD core conformations in gp120 variants (residues 421–433) complexed with soluble CD4 and antibody 17b (cyan; 1GC1) and gp120 (extended core) without a ligand (purple; 3TGQ, 3TGR, 3TGT, 3TIH).
The N276 glycosylation site is required for HIV-1 neutralization by the CD4 binding site specific HJ16 monoclonal antibody.
(2013) PLoS One 8
PubMed: 23874792 | PubMedCentral: PMC3714269 | DOI: 10.1371/journal.pone.0068863
Structural Analyses The crystal structure coordinates of the different gp120 molecules interacting with sCD4 (pdb 1gc1) or the human CD4bs-specific antibodies PGV04 (pdb 3se9), b12 (pdb 3dnl) and VRC0... (pdb 3ngb) were used to identify the footprint of interaction of each ligand on gp120 within an interaction distance of 5 A°.
In blue are shown the footprints of CD4 (pdb accession n° 1gc1) and the CD4bs-specific antibodies PGV04 (pdb n°: 3se9), b12 (pdb n°: 3dnl), and VRC01 (pdb n°: 3ngb).
Publication Year: 2013
Epitope specificity of human immunodeficiency virus-1 antibody dependent cellular cytotoxicity [ADCC] responses.
(2013) Curr HIV Res 11
PubMed: 24191939 | PubMedCentral: PMC3878369 | DOI: null
X-ray coordinates of (A) the unliganded gp12093TH057 coree (PDB:3TGT) and (B) the gp120HXBc2core/s CD4 subset of gp120HXBc2core/CD4/17b complex (PDB:1GC1) were fitted into tomograms using Chimera ...
Critical amino acids within the human immunodeficiency virus type 1 envelope glycoprotein V4 N- and C-terminals contribute to virus entry.
(2014) PLoS One 9
PubMed: 24465884 | PubMedCentral: PMC3897638 | DOI: 10.1371/journal.pone.0086083
Computational Analysis of the Mutants To gain insights into how these mutations significantly affect viral infectivity or cleavage of Env, we modeled the structures of HXB2-wt and the mutants 390L/G, ... 91F/A, 414I/G, and 416L/G (the pseudovirus infectivity of which was significantly reduced, Figure 3 ), according to the crystal structure of an HIV gp120 Env glycoprotein in complex with sCD4/17b (PDB code 1GC1)  ( Figures 5 and 6 ).
The three-dimensional structure of HXB2 gp120 complexed with sCD4 and the CD4i-specific mAb 17b (PDB code:1GC1) is shown.
Publication Year: 2014
Surfactant protein D inhibits HIV-1 infection of target cells via interference with gp120-CD4 interaction and modulates pro-inflammatory cytokine production.
PubMed: 25036364 | PubMedCentral: PMC4103819 | DOI: 10.1371/journal.pone.0102395
( i ) SP-D trimer (light green, dark green and orange cartoon) interacting with HIV-1 gp120 (grey cartoon) ( ii ) SP-D trimer (green) bound proximal to the CD4 binding region of gp120 (PDB ID: 1GC1).
(D) Protein Docking The structures of human lung surfactant protein D (PDB ID: 1PW9)  in the trimeric form and HIV-1 envelope glycoprotein gp120 complexed with two-domain fragment of human CD4 receptor (PDB ID: 1GC1) modeled with glycans  were docked using PatchDock server with default parameters  .
PubMed ID is not available.
Published in 2014
To illustrate the CD4 binding site on the trimer, a crystal structure of gp120 core in complex with CD4 (PDB ID 1GC1) was superimposed with the SOSIP trimer and CD4 footprint was projected on the surf... ce of the gp120 trimer.
Well-ordered trimeric HIV-1 subtype B and C soluble spike mimetics generated by negative selection display native-like properties.
(2015) PLoS Pathog 11
PubMed: 25569572 | PubMedCentral: PMC4287557 | DOI: 10.1371/journal.ppat.1004570
Bottom panel displays top and side views of the four-domain soluble CD4-liganded SOSIP trimers with the sCD4-bound gp120 core crystal structure (PDB ID 1GC1, gp120 in blue and sCD4 in red) fitted in t... e EM density.
Publication Year: 2015
Directed evolution of a yeast-displayed HIV-1 SOSIP gp140 spike protein toward improved expression and affinity for conformational antibodies.
(2015) PLoS One 10
PubMed: 25688555 | PubMedCentral: PMC4331506 | DOI: 10.1371/journal.pone.0117227
The CD4-binding site was determined using PyMol interface residues script on gp120-CD4 co-crystal structure PDB ID: 1GC1 and mapped to the corresponding side chains on 4NCO.
Published in 2015
Contacts with CD4 (yellow) and Fabs (green) are shown as transparent surfaces (modeled relative to the gp120 core from PDB: 1GC1) 24 .
The gp120 structure (1GC1) [ 21 ] in non-glycosylated state was acquired from the Protein Data Bank (PDB) [ 22 ].
Docked pose of gp120 with X5 in surface generated (a) and ribbon format (b); both H and L chains are shown in the figure with their residual interactions as reported in 1GC1.
X-ray crystal structure of the partially glycosylated HIV-1 HXBc2 gp120 (PDB 1GC1 [ 45 ]) was superimposed on unliganded gp120 electron tomography structure (PDB 3DNN [ 34 ]).
Spatial location of the R53 epitope in gp120 structures After an examination of all currently available gp120 structures in the RCSB PDB, we found that the region of the R53 epitope can form four dist... nct conformations ( Figure 5 ): (i) the CD4-bound (represented by the first gp120 core structure with PDB ID 1GC1.
Punica granatum (Pomegranate) juice provides an HIV-1 entry inhibitor and candidate topical microbicide.
(2004) BMC Infect Dis 4
PubMed: 15485580 | PubMedCentral: PMC533885 | DOI: 10.1186/1471-2334-4-41
The CD4 domains and the antigen-binding fragment of a neutralizing antibody were excised from the structure of the gp120-CD4-antibody complex  (1gc1 retrieved from the Protein Data Bank (pdb) [htt... ://www.rcsb.org/pdb/).
Publication Year: 2004
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