Citations in PubMed

Primary Citation PubMed: 7500345 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 1

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

Modeling and structural analysis of PA clan serine proteases.

(2012) BMC Res Notes 5

PubMed: 22624962 | PubMedCentral: PMC3434108 | DOI: 10.1186/1756-0500-5-256

For P. furiosus (Table 3 ), the matched structures were superposed with respect to a selected set of Cα atoms (43% superposition), with the structure 1GBI (an α-lytic protease from the... proteobacterium Lysobacter enzymogenes ) having the best score of 3.41 (RMSD values were between 0.357 and 0.563 Å, which helped to identify common segments corresponding to structurally conserved regions).

From these superposed structures, the variable loop regions were identified on the starting scaffold derived from 1GBI.

Table 2 SWISS MODEL homology results of Plasmodium falciparum PA serine protease target sequence with known PDB structures PDB ID Resolution Å R-value Score (bits) Expect value AA identity (%) 1L1JB 2.80 0.228 55.5 5 × 10 -9 38 1L1JA 2.80 0.228 55.5 5 × 10 -9 38 2AS9B 1.70 0.213 41.2 8 × 10 -5 29 2AS9A 1.70 0.213 41.2 8 × 10 -5 29 Table 3 LOOPP server results for secondary structure matches of Pyrococcus furiosus , Neurospora crassa and Arabidopsis thaliana PA serine protease target sequence with known PDB structures PDB ID Secondary structure     Score Sequence identity (%) Length (%)   Helical structure (%) Extended (%) Loops /Other (%)       P. furiosus Target 2.70 31.76 65.54 - - - 1GBI 0.00 52.41 47.59 3.410 27.14 94.59 1SSX 0.00 55.84 44.16 3.394 27.14 94.59 1GBM 0.00 55.17 44.83 3.357 27.14 94.59 1BOQ 0.00 52.41 47.59 3.343 27.14 94.59 1GBD 0.00 55.17 44.83 3.292 27.14 94.59 N. crassa Target 0.65 40.00 59.35 - - - 1VCW 2.60 33.77 63.64 3.078 23.87 93.55 1L1J 1.94 31.07 66.99 2.863 28.39 96.13 1TE0 2.74 32.19 65.07 2.742 24.66 87.74 1SOZ 0.00 33.51 66.49 2.535 22.73 93.55 1SOT 2.63 33.55 63.82 2.511 24.50 90.97 A. thaliana Target 0.00 38.60 61.40 - - - 1L1J 2.34 32.71 64.95 6.423 44.44 92.40 1VCM 3.03 35.76 61.21 6.247 42.69 92.40 1TE0 3.03 33.33 63.64 6.134 42.11 92.40 1Y8T 5.03 39.11 55.87 5.739 44.44 91.81 1SOZ 0.51 34.52 64.97 5.315 42.69 92.40 Table 4 Backbone refinement of the modeled PA proteases from Plasmodium falciparum , Pyrococcus furiosus, Neurospora crassa and Arabidopsis thaliana Structural model φ-ψ distribution in the regions of Ramachandran’s plot   Number of residues (percentage)   Most favoured Additional allowed Generously allowed Disallowed P. falciparum         Before backbone refinement 89(76.1%) 21(17.9%) 4(3.4%) 3(2.6%) After backbone refinement 84(71.9%) 33(28.2%) 0 (0.0%) 0 (0.0%) P. furiosus         Before backbone refinement 62(56.9%) 40(36.7%) 1(0.9%) 6(5.5%) After backbone refinement 84(71.8%) 33(28.2%) 0 (0.0%) 0 (0.0%) N. crassa         Before backbone refinement 65(52.0%) 50(40.4%) 4(3.4%) 3(2.6%) After backbone refinement 69(55.5%) 56(44.8%) 0 (0.0%) 0 (0.0%) A. thaliana         Before backbone refinement 82(60.7%) 45(32.6%) 7(4.4%) 3(2.2%) After backbone refinement 86(63.7%) 49(36.3%) 0 (0.0%) 0 (0.0%) Table 5 Structural validation of the modeled PA proteases from Plasmodium falciparum , Pyrococcus furiosus, Neurospora crassa and Arabidopsis thaliana Structural model All atom clashscore (No/1000 atoms) Rotamer outliers (%) RMSD of bond Length (Å) RMSD of bond angle (Degree) X-ray structure (1L1J) 4.33 7.49 0.029 2.74 Homology model of P. falciparum protease 1.86 5.26 0.030 3.14 X-ray structure (1GBI) 10.14 3.53 0.019 3.25 Threading model of P. furiosus protease 15.00 2.63 0.019 3.21 X-ray structure (1VCW) 3.23 4.58 0.024 3.91 Threading model of N. crassa protease 5.38 8.47 0.020 3.37 X-ray structure (1L1J) 4.33 7.49 0.029 2.74 Threading model of A. thaliana protease 11.50 8.79 0.018 3.31   Average Verify3D-1D Normalized 3D Profile ProSA ERRAT   score score (log 2 (Verify3D/L 2 ) Z-score quality Factor (%) X-ray structure (1L1J) 0.46 -10.95 -8.43 79.4 Homology model of P. falciparum protease 0.22 -9.28 -3.24 61.8 X-ray structure (1GBI) 0.48 -8.93 -6.73 81.6 Threading model of P. furiosus protease 0.19 -9.52 -3.27 71.2 X-ray structure (1VCW) 0.38 -12.80 -7.73 80.6 Threading model of N. crassa protease 0.24 -9.32 -3.81 52.6 X-ray structure (1L1J) 0.46 -10.95 -8.43 79.4 Threading model of A. thaliana protease 0.27 -9.33 -4.75 87.6 Catalytic Core Geometry Superposition of the P. falciparum P. furiosus N. crassa and A. thaliana PA proteases on the representative 1SGI protease structure found that 13 to 20% of the Cα atoms superposed with a RMSD below 2Å (Table 6 ).

Publication Year: 2012