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PDB ID Mentions in PubMed Central

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LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.

(2006) BMC Struct Biol 6

PubMed: 16995956 | PubMedCentral: PMC1601958 | DOI: 10.1186/1472-6807-6-19

Complex Unbound RMSD (Å) 1 Protein Description Ligand Description 2 1bid 3tms 0.24 Thymidylate synthase CBX, UMP 1cdo 8adh 1.17 Alcohol dehydrogenase NAD 1dwd 1hxf 0.44 Alpha thrombin + hirudi... MID 1fbp 2fbp 0.89 Phosphohydrolase AMP, F6P 1gca 1gcg 0.32 Galactose-binding protein GAL 1hew 1hel 0.21 Acetylchitotriose NAG 1hyt 1npc 0.87 Thermolysin DMS, BZS 1inc 1esa 0.21 Elastase ICL 1rbp 1brq 0.54 Retinol binding protein RTL 1rob 8rat 0.28 Ribonuclease A C2P 1stp 1swb 0.33 Streptavidin BTN 1ulb 1ula 0.61 Purine nucleoside phosphorylase GUN 2ifb 1ifb 0.37 Fatty acid binding protein PLM 3ptb 3ptn 0.26 Beta trypsin BEN 2ypi 1ypi 0.57 Triose phosphate isomerase PGA 4dfr 5dfr 0.80 Dihydrofolate reductase MTX 4phv 3phv 1.28 HIV 1 protease VAC 5cna 2ctv 0.44 Concanavalin A MMA 7cpa 8adh 2.17 Carboxypeptidase FVF 1a6w 1a6u 0.35 B1-8 FV fragment NIP 1apu 3app 0.36 Penicillopepsin MAN, OET, IVA, STA 1acj 1qif 0.34 Acetylcholinesterase THA 1blh 1djb 0.23 Methyl]phosphonate FOS 1byb 1bya 0.26 Beta amylase GLC 1hfc 1cge 0.37 Fibroblast collagenase HAP 1ida 1hsi 1.41 HIV 2 protease QND, HPB, PY2, PPL 1ivd 1nna 1.00 Sialidase FUC, ST1, NAG, MAN 1mrg 1ahc 0.30 Alpha momorcharin AND 1mtw 2tga 0.31 Trypsin DX9 1okm 4ca2 0.34 carbonic anhydrase II SAB 1pdz 1pdy 0.54 Enolase PGA 1phd 1phc 0.17 Camphor 5-monoxygenase HEM, PIM 1pso 1psn 0.33 Pepsin 3a IVA, STA 1qpe 3lck 0.25 Lck kinase PP2, PTR 1rne 1bbs 0.60 Renin NAG, C60 1snc 1stn 0.52 Staphylococcal nuclease PTP 1srf 1pts 0.45 Streptavidin MTB 1stp 2rta 0.62 Streptavidin BTN 2ctc 2ctb 0.15 Carboxypeptidase LOF 2h4n 2cba 0.33 Carbonic anhydrase II AZM 2pk4 1krn 0.63 Plasminogen kringle ACA 2sim 2sil 0.25 Sialidase (neuraminidase) DAN 2tmn 1l3f 0.62 Thermolysin PHO, NH2 3gch 1chg 0.91 Gamma chymotrypsin CIN 3mth 6ins 1.00 Methylparaben insulin MPB 5p2p 3p2p 0.62 Phosphilipase DHG 1imb 1ime 1.45 Inositol monophosphatase LIP 6rsa 7rat 2.08 Ribonuclease UVC 1 RMSD: Root mean square deviation of C α atoms after superimposing unbound structures on bound structures.

Complex Unbound LIGSITE csc 1 LIGSITE 2 PASS 3 SURFNET 4 CAST PDB Hits 5 D Near 6 Hits D Near Hits D Near Hits 7 D Near Hits D Near 1bid 3tms 1 3.4 1 2.0 1 3.9 1 3.9 1 3.1 1cdo 8adh 1 0.8 1 0.6 1 0.2 1 1.3 1 0.8 1dwd 1hxf 1 1.7 1 2.3 1 0.7 1 2.3 1 0.9 1fbp 2fbp 1 0.5 1 0.6 (2) 0.8 - - 1 1.5 1gca 1gcg 1 0.8 1 0.8 1 0.5 1 3.4 1 0.5 1hew 1hel 1 1.8 1 1.8 1 1.0 1 2.6 1 1.6 1hyt 1npc 1 1.2 1 1.1 1 1.7 1 1.0 1 0.7 1inc 1esa 1 2.9 3 0.8 - - 1 1.9 (10) 2.1 1rbp 1brq 1 0.9 1 0.9 1 0.9 (2) 1.6 1 1.0 1rob 8rat 1 0.9 2 1.0 1 0.3 1 1.7 1 1.6 1stp 1swb 1 0.6 1 0.3 1 0.8 1 2.4 1 1.4 1ulb 1ula - - (20) 3.2 - - 1 3.6 1 3.3 2ifb 1ifb 1 2.2 1 2.2 1 2.5 1 2.3 1 2.1 3ptb 3ptn 1/2 1.1 2 1.0 (2) 0.5 (2) 1.7 1 0.9 2ypi 1ypi - 3.0 2 3.0 (3) 2.2 - - (2) 2.7 4dfr 5dfr 1 1.9 1 3.5 1 2.3 - - 1 4.5 4phv 3phv 1 2.7 1 2.6 - - 1 2.9 1 2.6 5cna 2ctv 1/11 1.0 (13) 1.0 (2) 0.8 (6) 1.1 (6) 1.0 7cpa 5cpa 1 1.0 1 1.1 1 1.3 1 1.6 (3) 1.0 1a6w 1a6u 1/3 0.5 (4) 1.4 - - - - 1 1.4 1acj 1qif - 3.5 - 3.6 1 1.9 - - (40) 3.9 1apu 3app - 1.2 - 1.9 - - 1 3.7 -(2) -(4.1) 1blh 1djb 1 0.7 2 1.2 1 2.4 (2) 3.9 (5) 0.8 1byb 1bya 1 2.5 1 2.8 (4) 1.1 -1 -(4.2) 1 2.4 1hfc 1cge 1 0.7 1 0.9 (3) 0.8 (3) 1.2 1 0.5 1ida 1hsi 1 3.4 1 2.9 (3) 1.0 1 1.0 1 1.6 1igj 1a4j /4 0.8 -(19) 2.9 - - - - - - 1imb 1ime 1 1.7 1 1.0 1 1.7 1 4.0 1 1.3 1ivd 1nna 1 1.4 1 1.1 1 3.5 (2) 0.9 1 1.9 1mrg 1ahc 1 1.9 1 1.9 - - 1 3.3 1 0.8 1mtw 2tga 1/5 2.8 -(7) 1.2 - - (7) 3.2 (8) 1.6 1okm 4ca2 1 2.2 1 1.6 - - (3) 2.2 1 2.1 1pdz 1pdy 1 2.6 1 3.1 1 1.7 - - (5) 1.0 1phd 1phc 1 0.7 1 1.2 1 1.8 (2) 1.4 1 1.3 1pso 1psn 1 0.8 1 1.6 1 1.6 -1 -(4.3) 1 2.1 1qpe 3lck 2 1.5 2 1.2 1 0.7 - - - - 1rne 1bbs 1 1.0 1 1.2 1 1.4 1 2.2 1 1.0 1snc 1stn 1 1.5 1 1.5 1 1.3 1 1.9 1 1.3 1srf 1pts 1 1.5 1 0.5 1 1.2 (5) 0.8 1 1.1 2ctc 2ctb 1 0.6 1 1.1 (2) 0.8 1 2.2 1 1.2 2h4n 2cba 1/2 1.0 2 1.0 - - (3) 1.2 (2) 1.2 2pk4 1krn 1/2 0.7 2 0.8 - - (2) 2.2 1 1.9 2sim 2sil 1/2 0.7 2 0.6 - - (2) 2.3 (2) 0.8 2tmn 1l3f - 2.1 - - - - 1 0.7 1 3.9 3gch 1chg 10 2.2 -(10) 2.2 1 0.9 (11) 1.5 (2) 2.5 3mth 6ins 9 3.8 -(9) 1.8 - - -(3) -(4.7) - - 5p2p 3p2p 1 1.3 1 1.6 1 1.8 (2) 1.6 (2) 1.5 6rsa 7rat 1/4 0.9 -(5) 1.1 1 1.1 1 0.6 1 0.9 1 Grid resolution: 1.0 Å; probe radius: 1.6 Å.

Acetylchitotriose (1hel) good prediction but only a small part of ligand atoms occupy the pocket sites.

Figure 2 Left : Hen egg-white lysozyme with its ligand Tri-N-Acetylchitotriose (PDB 1hel).

6b , on Acetylchitotriose (pdbcode 1hel), only a small part of ligand atoms occupy the pocket sites.

Publication Year: 2006


PocketPicker: analysis of ligand binding-sites with shape descriptors.

(2007) Chem Cent J 1

PubMed: 17880740 | PubMedCentral: PMC1994066 | DOI: 10.1186/1752-153X-1-7

Complex Unbound Protein Description Pocket Ligand 1 Other Ligands 2 1bid 3tms Thymidylate synthase UMP CBX 1cdo 8adh Alcohol dehydrogenase NAD zn 1dwd 1hxf Alpha thrombin MID chains i, l 1fbp 2fbp Fru... tose 1,6-bisphosphatase AMP F6P, mg 1gca 1gcg Glucose/galactose-binding protein GAL ca 1hew 1hel Hen egg white lysozyme NAG - 1hyt 1npc Thermolysin BZS DMS, ca, zn 1inc 1esa Elastase ICL ca, so4 1rbp 1brq Retinol binding protein RTL - 1rob 8rat Ribonuclease A C2P - 1stp 1swb Streptavidin BTN - 1ulb 1ula Purine nucleoside phosphorylase GUN so4 2ifb 1ifb Fatty acid binding protein PLM - 3ptb 3ptn Beta trypsin BEN ca 2ypi 1ypi Triose phosphate isomerase PGA - 4dfr 5dfr Dihydrofolate reductase MTX ca, cl 4phv 3phv HIV 1 protease VAC - 5cna 2ctv Concanavalin A MMA ca, cl, mn 7cpa 5cpa Carboxypeptidase A FVF zn 1a6w 1a6u B1-8 FV fragment NIP - 1acj 1qif Acetylcholinesterase THA - 1apu 3app Penicillopepsin [IVA-VAL-VAL-STA-OET] MAN 1blh 1djb Beta-lactamase FOS - 1byb 1bya Beta amylase GLC so4 1hfc 1cge Fibroblast collagenase HAP ca, zn 1ida 1hsi HIV 2 protease [QND-VAL-HPB-PPL-PY2] - 1igj 1a4j Immunoglobulin DGX chain y 1imb 1ime Inositol monophosphatase LIP gd 1ivd 1nna Hydrolase ST1 FUC, NAG, MAN, ca 1mrg 1ahc Alpha momorcharin ADN - 1mtw 2tga Trypsin DX9 ca 1okm 4ca2 Carbonic anhydrase II SAB hg, zn 1pdz 1pdy Enolase PGA ace, mn 1phd 1phc Camphor 5-monoxygenase PIM HEM 1pso 1psn Pepsin 3a [IVA-VAL-VAL-STA-ALA-STA] - 1qpe 3lck Lck kinase PP2 PTR, so4 1rne 1bbs Renin C60 NAG 1snc 1stn Staphylococcal nuclease PTP ca 1srf 1pts Streptavidin MTB - 2ctc 2ctb Carboxypeptidase A LOF zn 2h4n 2cba Carbonic anhydrase II AZM zn 2pk4 1krn Plasminogen kringle ACA - 2sim 2sil Sialidase DAN - 2tmn 1l3f Thermolysin [PHO-LEU-NH2] ca, zn 3gch 1chg Gamma chymotrypsin CIN - 3mth 6ins Methylparaben insulin MPB cl, zn 5p2p 3p2p Phosphilipase DHG ca 6rsa 7rat Ribonuclease A UVC dod 1 Considered ligand defining the active site.

Complex Hits 1 D near /Å) 2 Unbound Hits 1 D near /Å) 2 1bid 1 2.7 3tms 1 2.3 1cdo 1 2.3 8adh 1 1.9 1dwd 1 0.5 1hxf 1 0.3 1fbp 1 1.3 2fbp 4 1.2 1gca 1 2.4 1gcg 1 1.4 1hew 1 1.4 1hel 1 1.2 1hyt 1 1.3 1npc 1 1.7 1inc 1 0.5 1esa (1) 4.1 1rbp 1 0.8 1brq 1 1.0 1rob 1 1.7 8rat 1 1.9 1stp 1 2.4 1swb 1 1.0 1ulb 1 1.0 1ula (1) 4.4 2ifb 1 1.7 1ifb 1 2.5 3ptb 1 0.4 3ptn 3 1.0 2ypi 5 1.0 1ypi (1) 4.8 4dfr (1) 7.8 5dfr 1 1.8 4phv 2 2.7 3phv 2 3.5 5cna - - 2ctv - - 7cpa 1 1.0 5cpa 1 1.1 1a6w 2 1.4 1a6u 3 1.2 1acj 1 0.8 1qif 2 1.2 1apu 1 0.6 3app 1 0.5 1blh 1 1.0 1djb 1 0.8 1byb 1 3.3 1bya 1 3.6 1hfc 1 1.2 1cge 1 1.0 1ida 1 1.5 1hsi 1 3.2 1igj 4 1.6 1a4j 3 1.4 1imb (1) 5.5 1ime 1 3.4 1ivd 2 1.7 1nna 1 1.5 1mrg (1) 5.8 1ahc (1) 5.2 1mtw 2 0.8 2tga 4 0.6 1okm 2 1.2 4ca2 1 1.6 1pdz 1 2.2 1pdy 1 2.7 1phd 1 1.1 1phc 1 0.9 1pso 1 0.4 1psn 1 1.1 1qpe 1 0.9 3lck 1 1.1 1rne 1 1.7 1bbs 1 0.7 1snc 1 2.1 1stn 1 0.3 1srf 1 0.5 1pts 1 0.6 2ctc 1 1.2 2ctb 1 1.5 2h4n 1 0.8 2cba 1 2.1 2pk4 2 0.7 1krn 1 0.7 2sim 2 0.6 2sil 2 0.4 2tmn 1 1.3 1l3f 1 1.1 3gch 1 0.8 1chg 2 1.5 3mth 2 0.8 6ins 2 1.3 5p2p 1 1.0 3p2p 1 0.8 6rsa 1 3.0 7rat 1 0.9 1 Rank of pocket centers within 4 Å of the considered ligand (brackets indicate hits exceeding the 4 Å criterion).

Publication Year: 2007


PEPOP: computational design of immunogenic peptides.

(2008) BMC Bioinformatics 9

PubMed: 18234071 | PubMedCentral: PMC2262870 | DOI: 10.1186/1471-2105-9-71

Table 2 Evaluation and comparison of the performances of PEPOP Ab – Ag complex 1 PDB Epitope (number of amino acids) PEPOP CEP DiscoTope Number of clusters containing epitopic residues/total n... mber of clusters Number of predicted residues of the epitope Sp Se PPV Sp Se PPV Sp Se PPV D1.3 – hen egg lysozyme [54] 1SFG_A 10 1/4 10 0.77 1.00 0.27 0.76 1.00 0.26 0.80 0.40 0.14 D44.1 – hen egg lysozyme [56] 1T6V_M 11 1/5 11 0.81 1.00 0.33 0.78 0.91 0.28 0.86 0.55 0.27 HyHEL-5 – hen egg lysozyme [57] 1VDP_B 14 1/5 13 0.83 0.93 0.41 0.88 0.00 0.00 0.78 0.00 0.00 Jel42 – HPr [60] 1POH 16 2/8 13 0.93 0.81 0.72 0.90 0.75 0.63 0.97 0.06 0.33 D11.15 – hen egg lysozyme [55] 1HEL 10 2/5 8 0.95 0.80 0.57 0.90 0.10 0.08 0.82 0.30 0.13 5G9 – tissue factor [61] 1WV7_T 18 1/3 14 0.75 0.78 0.25 0.84 0.28 0.15 0.84 0.17 0.10 BH151 – hemagglutinin [62] 5HMG_C 19 3/7 12 0.83 0.63 0.19 0.97 0.32 0.40 0.75 0.11 0.03 Bo2C11 – FVIII C2 domain [63] 1D7P_M 15 3/5 8 0.92 0.53 0.42 0.94 0.47 0.44 0.83 0.53 0.25 NC41 – neuraminidase [64] 1NMC_N 22 3/4 11 0.90 0.50 0.23 0.99 0.59 0.81 0.85 0.64 0.20 F9.13.7 – guinea fowl lysozyme [65] 1HHL 10 3/5 5 0.98 0.50 0.71 0.92 0.50 0.33 0.83 0.40 0.17 HyHEL-10 – hen egg lysozyme [58] 1UC0_A 16 3/5 8 0.99 0.50 0.89 0.96 0.56 0.64 0.87 0.44 0.32 HyHEL-63 – hen egg lysozyme [59] 1VFB_C 23 3/4 9 0.82 0.39 0.32 0.73 0.30 0.19 0.87 0.39 0.39 N10 – staphylococcal nuclease [66] 1EYO_A 18 3/6 6 0.87 0.33 0.29 0.88 0.06 0.07 0.66 0.33 0.13 Average 0.87 0.67 0.43 0.88 0.45 0.33 0.83 0.33 0.19 Median 0.87 0.63 0.33 0.90 0.47 0.28 0.83 0.39 0.17 1 The corresponding reference is given in parentheses nd: not determined (no results returned from the server) Sp: specificity; Se: sensibility; PPV: positive predictive value (see Materials and methods) Figure 2 Comparison of known epitopes with the predicted major cluster .

Publication Year: 2008


Molecular and functional characterization of a c-type lysozyme from the Asian corn borer, Ostrinia furnacalis.

(2009) J Insect Sci 9

PubMed: 19613460 | PubMedCentral: PMC3011828 | DOI: 10.1673/031.009.1701

Prediction of three-dimensional structure of OstrinLysC The three dimensional structure of OstrinLysC was predicted using the Swiss-PdbViewer v3.7 based on the known three dimensional structure of sil... worm lysozyme (1gd6A), ( Matsuura et al. 2002 ) and chicken lysozyme (1HEL) ( Wilson et al. 1992 ) as shown in Figure 7-A .

Publication Year: 2009


Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules.

(2014) BMC Biophys 7

PubMed: 25045516 | PubMedCentral: PMC4082500 | DOI: 10.1186/2046-1682-7-4

Protein preparation The crystal structure of hen egg white lysozyme (HEWL) was taken from the Protein Data Bank (ref): 1hel.

Publication Year: 2014