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PDB ID Mentions in PubMed Central Article count: 18

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PDB ID Mentions in PubMed Central

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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

Using 3DEX to map this mimotope to the HIV gp120 envelope glycoprotein [PDB: 1G9M], Schreiber et al reported that this mimotope might correspond to residues: L452, L453, T283, T455, N280, K282, and D2... 9.

Publication Year: 2006


Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm.

(2007) Nucleic Acids Res 35

PubMed: 17151070 | PubMedCentral: PMC1761437 | DOI: 10.1093/nar/gkl975

Algorithm flow In order to illustrate the algorithmic flow of PepSurf we first present a detailed description of the mapping of the monoclonal antibody (mAb) 17b epitope on the surface of gp120, the e... velope protein of HIV (dataset 1G9M in Table 1 ).

Figure 2 The prediction obtained by the PepSurf algorithm for the 17b–gp120 complex (PDB identifier 1G9M).

Peptides selected using the 17b, 13b5, Herceptin and Bo2C11 antibodies were mapped to the structure of their corresponding antigens, specified by the PDB identifiers 1G9M, 1E6J, 1N8Z and 1IQD, respectively ( Table 1 ).

This epitope has been previously determined by solving the 3D crystal structure of gp120 in complex with mAb 17b and CD4 [PDB identifier 1G9M; ( 24 )].

A surface graph was derived from the 238 solvent-exposed residues of gp120 (chain G; PDB 1G9M).

Publication Year: 2007


Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope.

(2007) PLoS Comput Biol 3

PubMed: 17238283 | PubMedCentral: PMC1779302 | DOI: 10.1371/journal.pcbi.0030011

Accession Numbers The accession numbers used in this paper are from Genbank ( http://www.ncbi.nlm.nih.gov/Genbank ) for [NNTSNNTSY outlier] subtype B sequence (M17451) and from Protein... Databank ( http://www.rcsb.org/pdb/home/home.do ) for folded CD4-bound gp120 protein (1G9M) and for HIV-1 glycoprotein gp120 (1G9M).

Publication Year: 2007


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


Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.

(2008) BMC Bioinformatics 9

PubMed: 18366628 | PubMedCentral: PMC2292695 | DOI: 10.1186/1471-2105-9-148

Binding affinities Binding affinities were calculated for 5 different ligand-protein systems taken from the PDB [ 54 ] and a number of their mutants: (i) tyrosine kinase Abl in complex with imatinib (... OPJ), (ii) Tyrosyl-tRNA synthetase in complex with tyrosine (4TS1), (iii) Aspartyl-tRNA synthetase in complex with aspartate (1IL2), (iv) Lysozyme in complex with the antibody HyHel-10 (3HFM) and (v) the complex of the glycoprotein CD4 with the gp120 component of the HIV virus (1G9M).

Publication Year: 2008


Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis.

(2008) BMC Bioinformatics 9

PubMed: 19087303 | PubMedCentral: PMC2639436 | DOI: 10.1186/1471-2105-9-538

In test cases three to eight, the six sets of mimotopes were obtained by screening phage display libraries with the 17b [ 22 ], 13b5 [ 22 ], Herceptin [ 40 ], Bo2C11 [ 41 ], Cetuximab Fab [ 42 ] and 8... D6A3 IgG [ 43 ] antibodies respectively (see Table 1 ), and their corresponding Ab-Ag complex structures have been resolved (PDB id: 1g9m , 1e6j , 1n8z , 1iqd , 1yy9 and 2adf ).

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqd 1yy9 2adf 1avz 1hx1 Average CED ID CE0179 CE0175 CE0058 CE0170 CE0096 CE0176 CE0199 CE0154 -- -- Epitope size 21 19 15 11 20 16 15 15 16 24 Antigen size 94 93 304 209 580 155 612 188 102 111 Pep-3D-Search TP/PE 19/40 7/13* 10/39 11/36 20/35* 6/47 10/25 12/36 10/39 13/39 MCC 0.3902 0.1442 0.1394 0.2285 0.1856 0.0356 0.1030 0.2153 0.1643 0.152 0.1758 Sensitivity 0.475 0.5833 0.2564 0.3056 0.5714 0.1277 0.4 0.3333 0.2564 0.3333 0.3642 Precision 0.9048 0.3684 0.6667 1.0 1.0 0.375 0.6667 0.8 0.625 0.5417 0.6948 PepSurf TP/PE 19/28 2/17 9/31 10/30 6/11 8/31 1/8* 10/18 14/25 12/25 MCC 0.4134 -0.0537 0.1257 0.2056 0.0596 0.1272 0.0067 0.1832 0.3348 0.1863 0.1589 Sensitivity 0.6786 0.1176 0.2903 0.3333 0.5455 0.2581 0.125 0.5556 0.56 0.48 0.3944 Precision 0.9048 0.1053 0.6 0.9091 0.3 0.5 0.0476 0.6667 0.875 0.5 0.5409 Mapitope TP/PE 19/22 2/18 13/33 1/6 9/13 15/106 3/23* 0/10 6/9* 5/21 MCC 0.4224 -0.062 0.1899 0.0154 0.0909 0.2401 0.0209 -0.0173 0.1387 0.0135 0.1053 Sensitivity 0.8636 0.1111 0.3939 0.1667 0.6923 0.1415 0.1304 0.0 0.6667 0.2381 0.3404 Precision 0.9048 0.1053 0.8667 0.0909 0.45 0.9375 0.1429 0.0 0.375 0.2083 0.4081 TP: number of true positives; PE: number of residues in the predicted epitope; TN: number of true negatives; FP: number of false positives; FN: number of false negatives; Matthews correlation coefficient ( MCC ) = ( T P ⋅ T N ) − ( F P ⋅ F N ) ( T P + F P ) ( T P + T N ) ( T N + F P ) ( T N + F N ) ; Sensitivity  ( Se ) = T P T P + F N ; Precision  ( Pr ) = T P T P + F P .

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqd 1yy9 2adf 1avz 1hx1 Average CA (distance threshold = 6.5) TP/PE 5/5 2/10 13/42 10/43 18/36* 7/31 2/10* 0/20 12/31 13/31 MCC 0.1119 -0.0014 0.1887 0.2033 0.1664 0.1015 0.019 -0.0367 0.262 0.1889 0.1204 Sensitivity 1.0 0.2 0.3095 0.2326 0.5 0.2258 0.2 0.0 0.3871 0.4194 0.3474 Precision 0.2381 0.1053 0.8667 0.9091 0.9 0.4375 0.1333 0.0 0.75 0.5417 0.4882 CA (distance threshold = 7) TP/PE 19/40 7/13* 10/39 11/36 20/35* 6/47 10/25 12/36 10/39 13/39 MCC 0.3902 0.1442 0.1394 0.2285 0.1856 0.0356 0.1030 0.2153 0.1643 0.152 0.1758 Sensitivity 0.475 0.5833 0.2564 0.3056 0.5714 0.1277 0.4 0.3333 0.2564 0.3333 0.3642 Precision 0.9048 0.3684 0.6667 1.0 1.0 0.375 0.6667 0.8 0.625 0.5417 0.6948 CA (distance threshold = 7.5) TP/PE 19/38 12/27* 10/45 9/33 18/40 0/36 7/25 12/36 9/37 9/36 MCC 0.3947 0.2349 0.1374 0.1812 0.1662 -0.0895 0.0704 0.2153 0.1332 0.0411 0.1485 Sensitivity 0.5 0.4444 0.2222 0.2727 0.45 0.0 0.28 0.3333 0.2432 0.25 0.2996 Precision 0.9048 0.6316 0.6667 0.8182 0.9 0.0 0.4667 0.8 0.5625 0.375 0.6126 CA (distance threshold = 8) TP/PE 20/39 12/28* 10/40 10/35 17/36 0/37 5/26 13/35 8/39 5/32 MCC 0.4248 0.2309 0.1391 0.2047 0.1565 -0.1144 0.0484 0.2378 0.0822 -0.065 0.1345 Sensitivity 0.5128 0.4286 0.25 0.2857 0.4722 0.0 0.1923 0.3714 0.2051 0.1563 0.2874 Precision 0.9524 0.6316 0.6667 0.9091 0.85 0.0 0.3333 0.8667 0.5 0.2083 0.5918 TP: number of true positives; PE: number of residues in the predicted epitope; TN: number of true negatives; FP: number of false positives; FN: number of false negatives; Matthews correlation coefficient ( MCC ) = ( T P ⋅ T N ) − ( F P ⋅ F N ) ( T P + F P ) ( T P + T N ) ( T N + F P ) ( T N + F N ) ; Sensitivity  ( Se ) = T P T P + F N ; Precision  ( Pr ) = T P T P + F P .

Furthermore, for the test cases 1jrh , 1g9m , 1e6j and 2adf , Pep-3D-Search and PepSurf gave better predictions, while Mapitope failed in the test cases 1e6j and 2adf .

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqd 1yy9 2adf 1avz 1hx1 Average CB (distance threshold = 6.5) TP/PE 5/5 0/0 11/43 11/38 15/30* 10/43 6/28 8/29 8/27 2/27 MCC 0.1119 0.0 0.155 0.2285 0.1379 0.1604 0.059 0.1316 0.1380 -0.1271 0.0995 Sensitivity 1.0 0.0 0.2558 0.2895 0.5 0.2326 0.2143 0.2759 0.2963 0.0741 0.3139 Precision 0.2381 0.0 0.7333 1.0 0.75 0.625 0.4 0.5333 0.5 0.0833 0.4863 CB (distance threshold = 7) TP/PE 13/18 6/9* 14/46 8/28 14/31* 9/46 9/29* 14/31 9/41 11/38 MCC 0.2747 0.1283 0.2048 0.1593 0.1282 0.127 0.0917 0.2604 0.1139 0.0939 0.1582 Sensitivity 0.7222 0.6667 0.3043 0.2857 0.4516 0.1957 0.3103 0.4516 0.2195 0.2895 0.3897 Precision 0.619 0.3158 0.9333 0.7273 0.7 0.5625 0.6 0.9333 0.5625 0.4583 0.6412 CB (distance threshold = 7.5) TP/PE 19/41 12/27 10/40 9/35 14/33** 2/45 8/28* 10/45 8/29 9/29 MCC 0.3879 0.2349 0.1391 0.1806 0.1279 -0.0837 0.0809 0.1626 0.13 0.084 0.1444 Sensitivity 0.4634 0.4444 0.25 0.2571 0.4242 0.0444 0.2857 0.2222 0.2759 0.3103 0.2978 Precision 0.9048 0.6316 0.6667 0.8182 0.7 0.125 0.5333 0.6667 0.5 0.375 0.5921 CB (distance threshold = 8) TP/PE 19/38 15/30 10/37 4/34* 18/37 4/42 7/26 10/18* 6/27 11/32 MCC 0.3947 0.3222 0.1401 0.0571 0.1664 -0.0101 0.0703 0.1832 0.0665 0.1271 0.1518 Sensitivity 0.5 0.5 0.2703 0.1176 0.4865 0.0952 0.2692 0.5556 0.2222 0.3438 0.3361 Precision 0.9048 0.7895 0.6667 0.3636 0.9 0.25 0.4667 0.6667 0.375 0.4583 0.5841 TP: number of true positives; PE: number of residues in the predicted epitope; TN: number of true negatives; FP: number of false positives; FN: number of false negatives; Matthews correlation coefficient ( MCC ) = ( T P ⋅ T N ) − ( F P ⋅ F N ) ( T P + F P ) ( T P + T N ) ( T N + F P ) ( T N + F N ) ; Sensitivity  ( Se ) = T P T P + F N ; Precision  ( Pr ) = T P T P + F P .

PDB ID Antibody Antigen References Library size * Antibody-antigen test cases 1jrh mAb A6 IFNgammaR Lang S et al.(2000) 59 × 5 1bj1 rhuMAb VEGF vascular endothelial growth factor ChenY et al. (1999) 36 × 6, 3 × 5, 2 × 4 1g9m mAb 17b gp120 Enshell-Seijffers D et al. (2003) 10 × 14,1 × 12 1e6j mAb 13b5 p24 Enshell-Seijffers D et al. (2003) 14 × 14, 2 × 7 1n8z Herceptin Fab Her-2 Riemer AB et al. (2004) 5 × 12 1iqd mAb Bo2C11 Coagulation factor VIII Villard S et al. (2003) 27 × 12 1yy9 Cetuximab Fab Epidermal Growth Factor Receptor Riemer AB et al. (2005) 4 × 10 2adf 82D6A3 IgG Von Willebrand factor Vanhoorelbeke K et al. (2003) 2 × 15, 3 × 6 Protein-protein test cases 1avz Fyn SH3 domain Nef Rickles RJ et al. (1994) 8 × 10, 10 × 12 1hx1 Bovine Hsc70 Bag chaperone regulator Takenaka IM et al. (1995) 8 × 15 *Number of sequences × sequence length.

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqds 1yy9 2adf 1avz 1hx1 Average AHA (distance threshold = 3.7) TP/PE 17/20 7/16 12/44 11/34 17/36* 6/32 6/25* 9/33 13/36 8/32 MCC 0.375 0.1243 0.1716 0.2286 0.1565 0.0733 0.0595 0.1502 0.2855 0.0351 0.1659 Sensitivity 0.85 0.4375 0.2727 0.3235 0.4722 0.1875 0.24 0.2727 0.3611 0.25 0.3667 Precision 0.8095 0.3684 0.8 1.0 0.85 0.375 0.4 0.6 0.8125 0.3333 0.6349 AHA (distance threshold = 4) TP/PE 16/20 7/10 13/42 8/30 15/30* 5/39 6/23 10/37 12/35 10/34 MCC 0.3491 0.1528 0.1887 0.1584 0.1379 0.0283 0.0598 0.1695 0.2525 0.0858 0.1583 Sensitivity 0.8 0.7 0.3095 0.2667 0.5 0.1282 0.2609 0.2703 0.3429 0.2941 0.3873 Precision 0.7619 0.3684 0.8667 0.7273 0.75 0.3125 0.4 0.6667 0.75 0.4167 0.6021 AHA (distance threshold = 4.3) TP/PE 16/18 8/11 14/42 8/36 17/30* 9/37 4/16* 11/37 10/33 4/26 MCC 0.3537 0.1773 0.2052 0.1558 0.1571 0.1431 0.0394 0.1923 0.1869 -0.0514 0.1559 Sensitivity 0.8889 0.7273 0.3333 0.2222 0.5667 0.2432 0.25 0.2973 0.303 0.1538 0.3986 Precision 0.7619 0.4211 0.9333 0.7273 0.85 0.5625 0.2667 0.7333 0.625 0.1667 0.6048 AHA (distance threshold = 4.6) TP/PE 19/36 9/24 9/44 4/41 18/38 0/34 8/25* 8/36* 5/37 6/27 MCC 0.3989 0.1483 0.1206 0.0495 0.1663 -0.1023 0.0813 0.1241 -0.0357 0.0051 0.0956 Sensitivity 0.5278 0.375 0.2045 0.0976 0.4737 0.0 0.32 0.2222 0.1351 0.2222 0.2578 Precision 0.9048 0.4737 0.6 0.3636 0.9 0.0 0.5333 0.5333 0.3125 0.25 0.4871 TP: number of true positives; PE: number of residues in the predicted epitope; TN: number of true negatives; FP: number of false positives; FN: number of false negatives; Matthews correlation coefficient ( MCC ) = ( T P ⋅ T N ) − ( F P ⋅ F N ) ( T P + F P ) ( T P + T N ) ( T N + F P ) ( T N + F N ) ; Sensitivity  ( Se ) = T P T P + F N ; Precision  ( Pr ) = T P T P + F P .

In order to evaluate the capability of the ACO algorithm for searching the target paths with various lengths on the antigen surface, we took gp120 (the envelope protein of HIV; chain G; PDB id: 1g9m ; the residue number of the antigen is 304, see Table 2 ) as the target antigen and randomly selected the paths with lengths from 9 to 25 (odd numbers) residues on the antigen surface as the search goals.

Publication Year: 2008


Prediction of antigenic epitopes on protein surfaces by consensus scoring.

(2009) BMC Bioinformatics 10

PubMed: 19772615 | PubMedCentral: PMC2761409 | DOI: 10.1186/1471-2105-10-302

Methods Protein datasets Protein Dataset 1 48 antigen-antibody complexes with resolution <3.0 Å were selected from the 59 representative antigen-antibody complexes compiled by Ponomare... ko and Bourne[ 25 ]: 2ADF , 1FE8 , 1BGX , 1E6J , 1EGJ , 1FSK , 1H0D , 1IQD , 1JRH , 1LK3 , 1MHP , 1NL0 , 1NSN , 1OAZ , 1ORS , 1PKQ , 1RJL , 1SY6 , 1TZI , 1WEJ , 1YJD , 1YY9 , 1ZTX , 2JEL , 1A14 , 1NCA , 1BVK , 1JHL , 1NDG , 1P2C , 1JPS , 1AR1 , 1EO8 , 1QFU , 1EZV , 1OSP , 1FJ1 , 1FNS , 1G9M , 1R3J , 1N8Z , 1NFD , 1TQB , 2VDL , 1V7M , 1XIW , 2AEP , and 1R0A .

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

(b) Surface representations of sCD4 from different gp120–sCD4–CD4i-Fab structures (PDB codes: HXBc2–sCD4–17b: 1G9M 5 ; YU2–sCD4–412d: 2QAD 3 ; JR-FL�... 013;sCD4–X5: 2B4C 4 ).

(c) Comparison of the CAP210–sCD4–21c structure with structures of sCD4–CD4i-Fab complexes including clade B gp120s (PDB codes 1G9M 5 , 2QAD 3 , 2B4C 4 for HXBc2–sCD4–17b, YU2–sCD4–412d, and JR-FL–sCD4–X5, respectively).

The core CAP210 structure was superimposed with the HXBc2, YU2, and JR-FL structures (PDB codes 1G9M 5 , 2QAD 3 , 2B4C 4 for HXBc2–sCD4–17b, YU2–sCD4–412d, and JR-FL–sCD4–X5, respectively) (top).

Publication Year: 2010


MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries.

(2011) BMC Bioinformatics 12

PubMed: 21609501 | PubMedCentral: PMC3124435 | DOI: 10.1186/1471-2105-12-199

In general, MimoPro performed better in 1ZTX, 2ADF and 2GHW but slightly worse in 1G9M and 1E6J than both PepSurf and Pep-3D-Search did.

PepSurf was the best performer in cases 1G9M, 1E6J, 3IU3 and 2NY7 but the worst in 1N8Z, 2ADF and 1ZTX, and even failed in 1N8Z*.

Publication Year: 2011


Analysis of conformational variation in macromolecular structural models.

(2012) PLoS One 7

PubMed: 22808083 | PubMedCentral: PMC3392262 | DOI: 10.1371/journal.pone.0039993

PDB ID Region of structural variation Structural manifestations in the variant region PSIPRED Prediction for variant region Disopred Prediction (Residue numbers) 1 3HRY/3K33 50–73: AALDAEFASLF... TLDSTNKELVNR α-helix in complex, turns and coil inindividual protein structure α-helix 72–73 2 3FII/1SFC 27–57: TSNRRLQQTQAQVDEVVDIMRVNVDKVLERD Largely unstructured in one complexand α-helix in another complex α-helix 28–36 3 1N7S/1XTG 167–204: MGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKMLG α-helix in one complex and largelyunstructured in the other α-helix 167–169, 171–173, 198, 204 4 3C98/3HD7 189–248: KQALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAV α-helix in one complex, unstructuredwith distorted helix in another complex α-helix 189, 248 5 2GRX/1IHR 164–182: PARAQALRIEGQVKVKFDV α-helix, β-strand in complex,β-strand in individual protein α-helix, β-strand 164–168 221–235: GSGIVVNILFKINGT Coil and β-strand in complex,β-strand in individual protein β-strand 221, 236 6 2JKR/2BP5 316–325: LAQKIEVRIP β-strand in one complex, unstructuredin the other β-strand 316–319 419–434: IKWVRYIGRSGIYETR β-strand in one complex, unstructuredin the other β-strand 431–434 7 1CDJ/1G9M 54–69: RADSRRSLWDQG α-helix in complex, turn in individualprotein α-helix 58–59, 62–64 12–18: VELTCTA β-strand in individual protein, coilin complex β-strand 12,18 8 3B2V/1IVO 19–32: FEDHFLSLQRMFNN α-helix in one complex and unstructuredin other α-helix 19,32 92–97: YALAVL β-strand in one complex and no electrondensity in other α-helix – 9 1BGW/2RGR 630–682: LQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELI α-helix in complex.

Perhaps coincidentally, an observation on the denaturation of β sheets at low pH [36] also correlates with the structure of the T-cell surface glycoprotein CD4 (PDB: 1CDJ, 1G9M) which shows well-defined β-strands when compared to its structure in complex with two other proteins where it is unstructured.

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).

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

The gp120 from HXBc2 in the b12 antibody-bound state (PDB ID: 2NY7) and the gp120 in complex with CD4 and 17b antibodies (pdb ID: 1G9M) were used in transition pathway calculations.

Publication Year: 2012


Viral escape from neutralizing antibodies in early subtype A HIV-1 infection drives an increase in autologous neutralization breadth.

(2013) PLoS Pathog 9

PubMed: 23468623 | PubMedCentral: PMC3585129 | DOI: 10.1371/journal.ppat.1003173

This simulated gp120 was modeled using all known CD4-bound gp120 structures (Protein Data Bank [PDB] accession numbers 1G9M [63] ,1RZK [22] , 2B4C [64] , 2NY7 [65] , 3JWD and 3JWO [66] , and 3LMJ [43]... ) as templates.

Publication Year: 2013


A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein.

(2013) PLoS Comput Biol 9

PubMed: 23696718 | PubMedCentral: PMC3656115 | DOI: 10.1371/journal.pcbi.1003046

Methods Homology modeling The missing regions of the structures for the YU2, HXB2, and CAP210 sequences (PDB accession numbers 1G9M [71] , 1RZK [70] , and 3LQA [44] ) lacking the V1–V3 loops w... re modeled using the MODELLER program [99] .

Publication Year: 2013


Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial.

(2013) PLoS One 8

PubMed: 24086607 | PubMedCentral: PMC3784573 | DOI: 10.1371/journal.pone.0075665

Properties of gp120 core structures All gp120 core PDB structure files (1G9M) [ 48 ], 1RZK [ 49 ], 2B4C [ 50 ], 2NY7 [ 51 ], 3JWD [ 52 ], 3JWO [ 52 ], and 3LQA [ 53 ] were prepared at pH=7 using the P... B 2PQR framework [ 54 ] with protonation states for all residues determined using PROPKA3.0 [ 55 ] program.

Publication Year: 2013


Dual-acting stapled peptides target both HIV-1 entry and assembly.

(2013) Retrovirology 10

PubMed: 24237936 | PubMedCentral: PMC3842668 | DOI: 10.1186/1742-4690-10-136

It is currently not clear what role each of these mutations plays in conferring resistance; the x-ray structure of gp120 (pdb:1G9M) shows that V120 and A327 are >27Å apart but they are... both on the CD4-binding interface of gp120 suggesting that they may play a significant role in HIV-1 entry.

Publication Year: 2013


Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms.

(2014) J Biomol Struct Dyn 32

PubMed: 23527883 | PubMedCentral: PMC3919177 | DOI: 10.1080/07391102.2013.770372

The structural templates for the CD4-bound and unliganded states of gp120 and for the V3 loop were crystal structures with PDB codes 1G9M (chain G) ( Kwong et al., 2000 ), 2BF1 ( Chen et al., 2005 ) 1... E4 ( Vranken, Budesinsky, Fant, Boulez, & Borremans, 1995 ), respectively.

Publication Year: 2014


Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: conversion of a viral entry agonist to an antagonist.

(2014) Acc Chem Res 47

PubMed: 24502450 | PubMedCentral: PMC3993944 | DOI: 10.1021/ar4002735

Figure 2 (A) The X-ray crystal structure of the CD4/gp120 core /Fab17b complex (PDB 1G9M).

Publication Year: 2014