Primary Citation PubMed: 9545299
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Structure-based predictive models for allosteric hot spots.
(2009) PLoS Comput Biol 5
PubMed: 19816556 | PubMedCentral: PMC2748687 | DOI: 10.1371/journal.pcbi.1000531
PDB of effector ligand-unbound (inactive state) PDB of effector ligand-bound (active state) Training Data Set Proteins CheY (signal transduction) 3chy 1fqw PurR repressor (transcription factor) 1dbq 1... et Tet repressor (transcription factor) 2trt 1qpi Hemoglobin (carrier protein/enzyme) 4hhb 1hho Phosphofructokinase (enzyme) 6pfk 4pfk phosphoglycerate dehydrogenase (enzyme) 1psd 1yba fructose-1,6-bisphosphatase (enzyme) 1eyj 1eyi Aspartate transcarbamoylase (enzyme) 1rac 1d09 RhoA (signal transduction) 1ftn 1a2b CDC-42 (signal transduction) 1an0 1nf3 glycogen phosphorylase (transcription factor) 1gpb 7gpb Independent Data Set Proteins glucokinase (enzyme) 1v4t 1v4s glutamate dehydrogenase (enzyme) 1nr7 1hwz lac repressor (transcription factor) 1tlf 1efa myosin II (motor protein/enzyme) 1vom 1fmw thrombin (enzyme) 1sgi 1sg8 Since the Michaelis constant, K M , has been shown to be an apparent dissociation constant, taking into account all substrate-bound species of enzyme, and is directly proportional to K S , we may replace K S with K M in (2)  .
Publication Year: 2009
Computing the protein binding sites.
(2012) BMC Bioinformatics 13 Suppl 10
PubMed: 22759425 | PubMedCentral: PMC3382440 | DOI: 10.1186/1471-2105-13-S10-S2
G proteins family in P-loop folds We select 5 proteins (1A2B, 1CXZ, 1DPF, 1FTN, 1S1C) from G proteins family in P-loop folds.
Publication Year: 2012
Identification of potential small molecule binding pockets on Rho family GTPases.
(2012) PLoS One 7
PubMed: 22815826 | PubMedCentral: PMC3397943 | DOI: 10.1371/journal.pone.0040809
We first carried out three 30 ns long cMD simulations, commencing from each of the three major conformational states (PDB codes for the initial structure models are 1A2B, 1FTN and 1LB1 for the GTP GDP... and APO states respectively, see Figure 2 ).
TC10 is regulated by caveolin in 3T3-L1 adipocytes.
PubMed: 22900022 | PubMedCentral: PMC3416860 | DOI: 10.1371/journal.pone.0042451
The structure of the C-terminal truncated, active GppNHp-bound TC10 (PDB code 2ATX) is shown, which mainly differs in the conformation of the Switch I region (orange) as superimposed on the Switch reg... ons of Cdc42 (1NF3; blue), Rac1 (1MH1; green) and RhoA (1A2B; red).
Model morphing and sequence assignment after molecular replacement.
(2013) Acta Crystallogr D Biol Crystallogr 69
PubMed: 24189236 | PubMedCentral: PMC3817698 | DOI: 10.1107/S0907444913017770
The fraction of residues assigned correctly for the structure 1a2b obtained using each template is shown.
The structure to be determined was that of human RhoA (PDB entry 1a2b ; Ihara et al. , 1998 ▶ ; the GTP analogue in the crystal was ignored in this test).
A set of 38 structures similar in sequence to 1a2b were identified by sequence alignment using HHpred (Söding, 2005 ▶ ) and were placed in the same location in the unit cell as 1a2b (DiMaio et al. , 2011 ▶ ).
These structures range from 7 to 36% sequence identity to 1a2b .
Each of these structures in turn was used as a template for morphing based on the structure factors for 1a2b , followed by autobuilding to obtain an improved map, trimming to match the new map and sequence assignment.
Publication Year: 2013
Generation of a single chain antibody variable fragment (scFv) to sense selectively RhoB activation.
(2014) PLoS One 9
PubMed: 25365345 | PubMedCentral: PMC4218836 | DOI: 10.1371/journal.pone.0111034
Molecular modeling All structures information were retrieved from the RCSB Protein Data Bank ( www.rcsb.org ): The PDB structure entry for active RhoAV14-GTPγS is 1A2B  .
A, The filling structure of active RhoAV14-GTPγS (Pdb code 1A2B) was created by UCSF-Chimera software  .
Publication Year: 2014
PubMed ID is not available.
Published in 2015
( c ) Superposition of the effector loops of GlcNAcylated RhoA with structures of non-glycosylated active GTPγS-bound RhoA (pdb code 1A2B) 42 and inactive GDP-bound RhoA (pdb code 1FTN) 41 .
Publication Year: 2015
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