Primary Citation PubMed: 9918722
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A reinforced merging methodology for mapping unique peptide motifs in members of protein families.
(2006) BMC Bioinformatics 7
PubMed: 16433931 | PubMedCentral: PMC1369005 | DOI: 10.1186/1471-2105-7-38
(B) The UPMs identified by RMA are labeled in blue on the crystal structures of mature human RNase1 (PDB: 1E21, 128 residues), RNase2 (PDB: 1GQV, 134 residues), RNase3 (PDB: 1DYT, 133 residues), RNase... (PDB: 1RNF, 119 residues), and RNase5 (PDB: 1B1I, 127 residues).
Publication Year: 2006
REMUS: a tool for identification of unique peptide segments as epitopes.
(2006) Nucleic Acids Res 34
PubMed: 16844991 | PubMedCentral: PMC1538771 | DOI: 10.1093/nar/gkl188
( a ) The PDB IDs of five members of human RNaseA superfamily (1e21:A, 1gqv:A, 1dyt:A, 1rnf:A and 1b1i:A) are imported to R E MUS.
In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach.
(2007) BMC Struct Biol 7
PubMed: 17559675 | PubMedCentral: PMC1913526 | DOI: 10.1186/1472-6807-7-37
The C α -RMSD between isolated (PDB entry 1B1I, resolution 1.8 Å) [ 42 ] and hRI-bound Ang (PDB entry 1A4Y, resolution 2.0 Å) is 1.07 Å.
Publication Year: 2007
Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications.
(2008) J Mol Biol 380
PubMed: 18508078 | PubMedCentral: PMC2582337 | DOI: 10.1016/j.jmb.2008.04.070
When aligned pairwise with hAng (PDB entry 1B1I ), 21 RNases ZF-1a and-3e deviate by 1.6 Å (rms) over 112 and 108 equivalent atoms, respectively; with RNase A (PDB entry 1RPG ), 22 the... corresponding figures are 1.5 Å and 1.8 Å over 107 and 112 equivalent atoms.
C α coordinates of RNase ZF-1a, RNase ZF-3e, mAng-4 (PDB entry 2J4T , chain A), 30 hAng (PDB entry 1B1I ), 21 RNase A·d(CpA) (PDB entry 1RPG ), 22 hRNase 4 (PDB entry 1RNF , chain A), 37 hECP·2′,5′-ADP (PDB entry 1H1H ), 24 hEDN (PDB entry 1GQV ), 23 hRNase 7 (PDB entry 2HKY , model no. 15), 25 RC-RNase·d(ACGA) (PDB entry 1M07 , chain A), 27 Amph-2 (PDB entry 2P7S ) 28 and ONC (PDB entry 1ONC ) 26 were aligned with CE-MC, 82 and a loop-based Hausdorff measure (LHM) of structural dissimilarity 31 was used to compute a pairwise distance matrix.
RNase ZF-1a, RNase ZF-3e and hAng (PDB entry 1B1I ) 21 were aligned with the RNase A·uridine vanadate complex (PDB entry 1RUV ) 86 on the basis of the C α positions of His12, Lys41, Thr45 and His119 in the latter.
Ribbon diagrams of (a) RNase ZF-1a, (b) RNase ZF-3e, (c) hAng (PDB entry 1B1I ) 21 and (d) RNase A·d(CpA) (PDB entry 1RPG ) 22 , the latter including ball-and-stick and space-filling representations of the dinucleotide inhibitor.
The C α coordinates of RNase ZF-1a, RNase ZF-3e, hAng (PDB entry 1B1I ) 21 and RNase A·d(CpA) (PDB entry 1RPG ) 22 were aligned with CE-MC.
86 b PDB entry 1B1I .
Publication Year: 2008
Mechanisms of loss of functions of human angiogenin variants implicated in amyotrophic lateral sclerosis.
(2012) PLoS One 7
PubMed: 22384259 | PubMedCentral: PMC3288110 | DOI: 10.1371/journal.pone.0032479
g001 Figure 1 Cartoon representation of X-ray structure for Human Angiogenin (PDB code: 1B1I).
Cartoon representation of the structure of Human Angiogenin (PDB entry 1B1I) showing its functional sites; catalytic triad residues are represented as stick models, nuclear localization signal is represented in magenta color and receptor binding site is represented in orange color.
Ribbon representation of structure of Human Angiogenin (PDB entry 1B1I) with mutational sites; mutations are labeled and represented as stick models in orange color.
Methods System setup The crystal structure of human angiogenin (PDB: 1B1I) was used as the starting point  .
Publication Year: 2012
Prediction of functional loss of human angiogenin mutants associated with ALS by molecular dynamics simulations.
(2013) Sci Rep 3
PubMed: 23393617 | PubMedCentral: PMC3566597 | DOI: 10.1038/srep01225
Methods Preparation of starting structures and MD simulations The X-ray crystal structure of human angiogenin 15 obtained from Protein Data Bank (PDB code: 1B1I) was used as the starting structure for... MD simulations.
All the reported ALS associated angiogenin (PDB ID: 1B1I) mutations are labeled and represented as stick model (lime green color).
Publication Year: 2013
Crystal structures of murine angiogenin-2 and -3-probing 'structure--function' relationships amongst angiogenin homologues.
(2013) FEBS J 280
PubMed: 23170778 | PubMedCentral: PMC3572582 | DOI: 10.1111/febs.12071
Ribbon diagrams of (A) mAng-2, (B) mAng-3, (C) mAng, (D) mAng-4, (E) hAng (PDB code: 1B1I) 49 and (F) RNase A (PDB code: 1RUV) 76 .
ANGDelMut - a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis-associated angiogenin mutations.
(2013) F1000Res 2
PubMed: 24555108 | PubMedCentral: PMC3901456 | DOI: 10.12688/f1000research.2-227.v3
The X-ray structure of human angiogenin (PDB code: 1B1I ) 14 is used as a starting structure to prepare the mutant, from which the crystallographic water and cofactor, citric acid (CIT) is removed whi... e keeping the secondary structure intact.
When the user submits an ANG mutation, for example K17I and/or L35P, the PyMOL molecular graphics system 25 is used to mutate residue K17 to I17 and L35 to P35 in the crystal structure of ANG (PDB ID: 1B1I without the heteroatoms) and the modified file is then saved in PDB format ( Figure 1 ).
Human antimicrobial peptides and proteins.
(2014) Pharmaceuticals (Basel) 7
PubMed: 24828484 | PubMedCentral: PMC4035769 | DOI: 10.3390/ph7050545
Shown are ( A ) RNase 3 (dimeric crystal structure, PDB ID: 4A2O); ( B ) RNase 3 (NMR structure, PDB ID: 2KB5); ( C ) RNase 5 (crystal structure, PDB ID: 1B1I); ( D ) RNase 5 (NMR structure, PDB ID: 1... WZ); ( E ) RNase 2 (crystal structure, PDB ID: 2BZZ); and ( F ) RNase 7 (NMR structure, PDB ID: 2HKY).
Publication Year: 2014
Computational and functional characterization of Angiogenin mutations, and correlation with amyotrophic lateral sclerosis.
(2014) PLoS One 9
PubMed: 25372031 | PubMedCentral: PMC4221194 | DOI: 10.1371/journal.pone.0111963
The D22G and L35P mutations in Angiogenin (PDB ID: 1B1I) are labeled and represented as stick models (red).
Materials and Methods Molecular modeling and MD simulations of wild-type and mutated Angiogenin The crystal structure of human Angiogenin (PDB: 1B1I) was used as the starting point.
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