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A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity.
(2012) PLoS One 7
PubMed: 22359655 | PubMedCentral: PMC3281107 | DOI: 10.1371/journal.pone.0032011
PDB P M EC L NATIVE FUNCTION POSSIBLE PROMISCUOUS FUNCTIONS 5CPA 1 Y 188.8.131.52 307 CARBOXYPEPTIDASE A cytochrome c peroxidase, pyruvate oxidase, thymidine phosphorylase, hexokinase pii, chloramphenicol... acetyltransferase 1MPY 0.9 Y 184.108.40.206 307 CATECHOL 2,3- DIOXYGENASE dipeptidyl peptidase iv soluble form, purple acid phosphatase, bacterial luciferase, phosphoinositide-specific phospholipase c, 1AQ2 0.85 N 220.127.116.11 540 PHOSPHOENOLPYRUVATE CARBOXYKINASE glutamate semialdehyde aminotransferase, endo/exocellulase e4, deoxycytidylate hydroxymethylase, aldolase carbamate carbamoylphosphate synthetase 1QZ9 0.84 Y 18.104.22.168 416 KYNURENINASE glycine n-methyltransferase, leucyl-trna synthetase, cysteinyl-trna synthetase, citrate synthase, cytochrome p450 2b4 1EHI 0.84 Y 22.214.171.124 377 D-ALANINE:D-LACTATE LIGASE ribonuclease alpha-sarcin, cytochrome p450 2b4, glutamate semialdehyde aminotransferase, ermc' methyltransferase, chitinase 5RSA 0.83 N 126.96.36.199 124 RIBONUCLEASE A thymidine phosphorylase, putative biotin ligase, nadh-dependent nitrate reductase, adenylosuccinate synthetase, carboxykinase 1I9A 0.77 Y 188.8.131.52 182 ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE acid beta-glucosidase, ribonuclease rh, chitinase a, purine nucleoside phosphorylase, leucyl-trna synthetase 1M9C 0.76 N 184.108.40.206 165 CYCLOPHILIN A nadh-dependent nitrate reductase, uracil phosphoribosyltransferase, cyclooxygenase-2, cytochrome c peroxidase, dehydrogenase 1ONE 0.74 Y 220.127.116.11 436 ENOLASE purine nucleoside phosphorylase, n-ethylmaleimide sensitive factor, oxygen-insensitive nadph nitroreductase, ribonuclease alpha-sarcin, biotin ligase 1GUM 0.63 N 18.104.22.168 222 GLUTATHIONE TRANSFERASE uracil phosphoribosyltransferase, phosphomannose isomerase, carboxykinase, tetrahydrodipicolinate n-succinyltransferase, biotin ligase P: Promiscuity index; M: Is a metal liganded by the active site in the crystal structure; EC - Enzyme Commission number; L: Sequence length.
Ribonuclease A (PDB id: 5RSA) is another example of an ancient multifaceted protein, that has been honed by evolution to maximum efficiency  .
Publication Year: 2012
Rapid and accurate prediction and scoring of water molecules in protein binding sites.
PubMed: 22396746 | PubMedCentral: PMC3291545 | DOI: 10.1371/journal.pone.0032036
Protein PDB codes Resolution (Å) Ligand HIV-Protease 3FX5, 1HPX, 2ZYE a 0.93, 2,1.9 KNI-272 Ribonuclease A 1KF5, 1FS3, 5RSA a 1.2, 1.4, 2 None GluR2 ligand binding core 1FTM b , 1MY2 b 1.7, 1.... AMPA Trypsin 1S0Q, 1UTQ, 1TPO 1.0, 1.2, 1.7 None Concanavalin A 1NLS, 1GKB, 1JBC, 1QNY a 0.9, 1.6, 1.2, 1.8 None Glutathione S-transferase 1K3Y b , 1K3L b 1.3, 1,5 S-hexyl glutatione Carbonic Anhydrase 3KS3, 3MWO, 2ILI 0.9, 1.4, 1.1 None a Structures that have been determined by neutron diffraction.
OneG: a computational tool for predicting cryptic intermediates in the unfolding kinetics of proteins under native conditions.
PubMed: 22412877 | PubMedCentral: PMC3296725 | DOI: 10.1371/journal.pone.0032465
The reliability of the program on predicting cis-trans proline conformations in proteins such as ubiquitin, RNase A (PDB ID: 5RSA) and cardiotoxin III is depicted in Table 2 .
Rigidity analysis of protein biological assemblies and periodic crystal structures.
(2013) BMC Bioinformatics 14 Suppl 18
PubMed: 24564201 | PubMedCentral: PMC3817814 | DOI: 10.1186/1471-2105-14-S18-S2
Indeed, it is reported in the literature [ 5 ] that the Ribonuclease A (RNase A) protein (PDB code 5RSA) retains its function even in the crystallized form used for its X-Ray structure determination.
For the Ribonuclease A protein (PDB file 5RSA), which is functionally active in the crystallized form, we found that the individual protein and its crystal form retain the flexibility parameters between the two states.
Rigidity analysis of Ribonuclease A - PDB files 5RSA and 9RSA Our last cast study is on Ribonuclease A, which we analyze based on two PDB files (5RSA and 9RSA).
Figure 10 For Ribonuclease A (PDB file 5RSA), which performs its function even in its crystalline form [ 5 ] , the asymmetric unit (a) and its unit cell (b) are largely flexible .
Publication Year: 2013
A local average distance descriptor for flexible protein structure comparison.
(2014) BMC Bioinformatics 15
PubMed: 24694083 | PubMedCentral: PMC3992163 | DOI: 10.1186/1471-2105-15-95
Figure 1 Flowchart of LAD profile generation for the protein 5rsa:A. (a) Yellow ribbons display the secondary structures and red spheres represent the backbone atoms (N, Cα, C, O) of each resi... ue.
(a) The structural alignment of 1a2w:A (green) and 5rsa:A (blue); the hinge loops are highlighted in red.
Figure 6 d and Figure 6 e have shown a high consistency of LAD ED and LAD GD profiles between open-form (PDB code: 1a2w, chain A) and close-form (PDB code: 5rsa, chain A) of Ribonuclease A respectively.
Figure 6 An example of self-connection case for domain swapping proteins of 1a2w:A and 5rsa:A. The yellow part of open-form Ribonuclease A (PDB code: 1a2w, chain A) swaps toward the protein body to form a closed-form (PDB code: 5rsa, chain A).
Publication Year: 2014
PubMed ID is not available.
Published in 2015
Different proteins (PDB Codes = 1L2K, 1L2N, 1NTP, 1VCX, 1WQ2, 2DXM, 2GVE, 2INQ, 2MB5, 2R24, 2VS2, 2WYX, 2YZ4, 2ZOI, 2ZWB, 2ZYE, 3A1R, 3BYC, 3HGN, 3INS, 3KKX, 3KMF, 3KYX, 3L45, 5PTI and 5RSA) whose str... ctures had been determined by neutron diffraction were analyzed for their hydrogen-bonding patterns.
Publication Year: 2015
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