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PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

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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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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.

Publication Year: 2008


ProteinShader: illustrative rendering of macromolecules.

(2009) BMC Struct Biol 9

PubMed: 19331660 | PubMedCentral: PMC2672931 | DOI: 10.1186/1472-6807-9-19

(C) A tube style display of the human growth hormone protein [PDB: 1HGU ], a four α-helix bundle structure [ 47 ], is shown in gray scale and using Phong lighting with a single directional lig... t and no specular highlighting.

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

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 ident... ty (%) 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.

Publication Year: 2009


VitAL: Viterbi algorithm for de novo peptide design.

(2010) PLoS One 5

PubMed: 20532195 | PubMedCentral: PMC2880006 | DOI: 10.1371/journal.pone.0010926

The PDB accession code of the protein is 1HGU [64] .

Publication Year: 2010


Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

(2011) BMC Bioinformatics 12

PubMed: 21831299 | PubMedCentral: PMC3166946 | DOI: 10.1186/1471-2105-12-334

Table 1 11 representative proteins - number of residues and number of atoms PDB4 Name Residue Range # residues # protein atoms 2adr Domain of Adr1 DBD from S. cerevisiae 102-130 29 496 1nr2 Thymus and... activation-regulated chemokine 8-69 62 1011 1okt Glutathione S-transferase 1-85 85 1412 2tgi Domain of transforming growth factor-beta 2 (TGF- B2) 1-112 112 1750 1d0n Horse plasma gelsolin 27-159 133 2095 1bp5 Domain of serum transferrin 82-246 165 2487 1hgu Human growth hormone 2-190 189 3011 1p88 3-phosphoshikimate 1-carboxyvinyltransferase 25-240 216 3272 1fzw Monomer of glucose-1-phosphate thymidylyltransferase 2-293 292 4560 1qaz Alginate Lyase A1-III 4-354 351 5495 1ehe Cytochrome P450nor 5-403 399 6217 Figure 3 Comparison of heavy-atom contacts query with and without spatial indexing for 11 metafold representatives over 1 ns .

Publication Year: 2011


Genetic and structural characterization of the growth hormone gene and protein from tench, Tinca tinca.

(2012) Fish Physiol Biochem 38

PubMed: 22660840 | PubMedCentral: PMC3494871 | DOI: 10.1007/s10695-012-9661-x

However, the tench GH sequence also showed significant similarity to six human growth hormone sequences with described 3D structures, PDB ID: 1HWG, 1KF9, 1HWH, 1HHR, 1HGU and 1AXI.

Publication Year: 2012


Pierced Lasso Bundles are a new class of knot-like motifs.

(2014) PLoS Comput Biol 10

PubMed: 24945798 | PubMedCentral: PMC4063663 | DOI: 10.1371/journal.pcbi.1003613

Methods S tructure B ased M odels (SBMs) In this work we used a Cα SBMs [66] , [67] to investigate the folding of eight helical cytokines, including five PLB proteins (PDB code 1AX8, 3PIV, 3PI... , 1JLI and 2L3O) and three unthreaded four-helix bundles (1RHG, 1EMR and 1HGU).

Publication Year: 2014