Citations in PubMed

Primary Citation PubMed: 3586017 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme.

(2011) J Am Chem Soc 133

PubMed: 22092261 | PubMedCentral: PMC3244821 | DOI: 10.1021/ja207914y

Table 1 Rankings of Hot Spots Identified by FTMap and Their Respective Numbers of Probe Clusters       secondary sites a     PDB entry structural notes site C a... site B site D total probe cluster count distance to CCN (Å) b 2LYO holo, CCN bound 1 (34), 6 (4) 3 (13) 2 (16) 67 1.1 2LYM apo 1 (22), 3 (13), 6 (6) 2 (15), 7 (5) 4 (12) 73 1.4 1IR8 Ile58 → Met58 1 (33), 7 (2) 3 (11), 5 (10) 2 (14) 67 1.6 1IR9 Ile98 → Met98 1 (25), 6 (6) 2 (18) 4 (11) 60 2.5 1LSY Asp52 → Ser52 1 (34), 6 (5) 2 (13) 3 (12) 64 1.3 1LSZ Asp52 → Ser52, holo 1 (32), 8 (3) 2 (11), 4 (10) 3 (11), 5 (6) 73 1.2 1XEI 17.6% dehydrated 1 (34) 4 (11) 2 (14) 59 1.1 1XEJ 16.9% dehydrated 1 (35), 6 (6)   4 (10) 51 0.7 1XEK 9.4% dehydrated 1 (18), 5 (7), 9 (4)   3 (12) 41 1.3 a The number shown in parentheses after each ranking number is the total probe cluster count for that particular CS.

Thus, FTMap identified residues in both the primary and secondary hot spots that are important for ligand binding, in contrast to the other two computational methods, which restricted consideration to site C. 14 , 15 Figure 3 Distributions of nonbonded interactions between HEWL residues and the probes in the CSs shown in Table 1 from the mapping of the apo structure 2LYM (black) and between the HEWL residues and eight representative ligands from PDB files 1LZB , 1LZC , 1AT6 , 1HEW , 1SF6 , 1SF7 , 1SFB , and 1SFG (gray).

Figure 4 Mapping results for the 2LYM structure using FTMap (A) are shown in comparison to those obtained using MD simulations on the 2LYO structure (B).

( 3 ) Figure 1 Centers of probe clusters found by mapping the HEWL apo structure (PDB entry 2LYM ) using FTMap.

In short, the structure derived from PDB entry 2LYO corresponds to the experiment of Wang et al.,( 13 ) with the singly bound CCN molecule residing in site C; the corresponding apo structure is also listed (PDB entry 2LYM ).

Centers of probe clusters (shown as sticks) for (A) the apo structure 2LYM and (B) the structure 1XEK with the smallest binding cavity.

Publication Year: 2011


Protein molecular surface mapped at different geometrical resolutions.

(2013) PLoS One 8

PubMed: 23516572 | PubMedCentral: PMC3597524 | DOI: 10.1371/journal.pone.0058896

Protein name PDB code Atoms Residues Chains 1 1 α lactalbumin 1A4V 1092 123 1 2 2 porcine β-lactoglobulin 1EXS 1248 160 1 3 bovine β-lactoglobulin 1BEB 2473 324 2 3, Subset 3.1... RMSD(129) = 0.6481 4 hen egg-white lysozyme 1LYZ 1001 129 1 5 turkey egg-white lysozyme 135L 994 129 1 6 hen egg-white lysozyme 2LYM 1001 129 1 7 triciclic lysozyme 2LZT 1001 129 1 3, Subset 3.2 RMSD(164) = 0.24 8 mutant of phage T4 lysozyme 1L35 1305 164 1 9 T4 lysozyme 1LYD 1309 164 1 4 RMSD(124) = 0.1655 10 ribonuclease-A 8RAT 951 124 1 11 ribonuclease-A 1RBX 956 124 1 12 bovine ribonuclease-A 3RN3 957 124 1 13 ribonuclease-A 1AFU 1894 248 2 5, Subset 5.1 RMSD(287)  = 0.8877 14 human oxyhemoglobin 1HHO 2192 287 2 15 human carbonmonoxy hemoglobin 2HCO 2192 287 2 16 horse deoxyhemoglobin 2DHB 2201 287 2 5, Subset 5.2 RMSD(574)  = 1.501 17 human hemoglobin A 1BUW 4342 574 4 18 human hemoglobin (W37A) 1Y4F 4368 574 4 19 hemoglobin mutant (W37A) 1A01 4368 574 4 20 human hemoglobin (W37E) 1Y4P 4376 574 4 21 hemoglobin mutant (W37Y) 1A00 4382 574 4 22 human hemoglobin (W37Y) 1Y46 4382 574 4 23 human deoxyhemoglobin 2HHB 4384 574 4 24 human hemoglobin (W37G) 1Y4G 4366 574 4 25 hemoglobin mutant (V1M) 1A0U 4386 574 4 26 hemoglobin mutant (V1M) 1A0Z 4386 574 4 27 recombinant hemoglobin 1C7D 4396 576 3 6 RMSD(585) = 2.3740 28 human serum albumin complexed with octadecanoic acid 1E7I 4496 585 1 29 recombinant human serum albumin 1UOR 4617 585 1 30 human serum albumin 1E78 4302 585 1 31 human serum albumin 1AO6 4600 585 1 32 human serum albumin 1BM0 4600 585 1 7 33 immunoglobulin 1IGY 10002 1294 4 34 immunoglobulin 1IGT 10196 1316 4 35 intact human IgG B12 1HZH 10355 1344 4 To quantify the similarity between the members of a class, for all sets, or subsets, i.e., for lysozyme and hemoglobins, the Root-Mean-Square Deviation (RMSD) has been calculated using the protein structure comparison service Fold at the European Bioinformatics Institute ( http://www.ebi.ac.uk/msd-srv/ssm ).

Publication Year: 2013


Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

(2014) J Phys Chem B 118

PubMed: 24479585 | PubMedCentral: PMC4103960 | DOI: 10.1021/jp409805p

Table 1 Protein Molecular Weight, Secondary Structure in Terms of Helical and β-Sheet Composition, Surface Composition in Terms of the Total Time-Averaged OH-Bond Population of the Hydrophobe,... H-Bond Donor or H-Bond Acceptor Sites, and Total Charge     secondary structure relative OH-bond population     molecular weight (kDa) helical β-sheet hydrophobe donor acceptor total charge ubiquitin 9 23% 34% 68% 15% 17% 0 lysozyme 14 40% 10% 72% 15% 13% +8 subtilisin Carlsberg 27 28% 19% 71% 13% 16% –1 acetylcholinesterase 59 36% 17% 74% 14% 12% –9 The initial protein configurations were obtained from the crystallographic structures with PDB codes 4ARA (acetylcholinesterase), 1SCN (subtilisin Carlsberg), 2LYM (lysozyme), and 1UBQ (ubiquitin).

Publication Year: 2014


Mapping hydrophobicity on the protein molecular surface at atom-level resolution.

(2014) PLoS One 9

PubMed: 25462574 | PubMedCentral: PMC4252106 | DOI: 10.1371/journal.pone.0114042

Protein name PDB code Atoms Residues Chains 1 1 α lactalbumin 1A4V 1092 123 1 2 2 porcine β-lactoglobulin 1EXS 1248 160 1 3 bovine β-lactoglobulin 1BEB 2473 324 2 3 4 chicken e... g-white lysozyme 1LYZ 1001 129 1 5 turkey egg-white lysozyme 135L 994 129 1 6 hen egg-white lysozyme 2LYM 1001 129 1 7 triciclic lysozyme 2LZT 1001 129 1 8 mutant phage T4 lysozyme 1L35 1305 164 1 9 T4 lysozyme 1LYD 1309 164 1 4 10 ribonuclease-A 8RAT 951 124 1 11 ribonuclease-A 1RBX 956 124 1 12 bovine ribonuclease-A 3RN3 957 124 1 13 ribonuclease-A 1AFU 1894 248 2 5 14 human oxyhemoglobin 1HHO 2192 287 2 15 human carbonmonoxy hemoglobin 2HCO 2192 287 2 16 horse hemoglobin 2DHB 2201 287 2 17 human hemoglobin A 1BUW 4342 574 4 18 human hemoglobin 1Y4F 4368 574 4 19 hemoglobin mutant 1A01 4368 574 4 20 human hemoglobin 1Y4P 4376 574 4 21 hemoglobin mutant 1A00 4382 574 4 22 human hemoglobin 1Y46 4382 574 4 23 human deoxyhemoglobin 2HHB 4384 574 4 24 human hemoglobin 1Y4G 4366 574 4 25 hemoglobin mutant 1A0U 4386 574 4 26 hemoglobin mutant 1A0Z 4386 574 4 27 recombinant hemoglobin 1C7D 4396 576 3 6 28 human serum albumin complex with octadecanoic acid 1E7I 4496 585 1 29 recombinant human serum albumin 1UOR 4617 585 1 30 serum albumin 1E_78 4302 585 1 31 human serum albumin 1AO6 4600 585 1 32 human serum albumin 1BM0 4600 585 1 7 33 immunoglobulin 1IGY 10002 1294 4 34 immunoglobulin 1IGT 10196 1316 4 35 intact human IgG B12 1HZH 10355 1344 4 Note: The proteins marked in bold are model proteins and those in italics have been also used for the analysis of statistical strength.

Publication Year: 2014