Citations in PubMed

Primary Citation PubMed: 11106734 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 12

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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Protein structure similarity from Principle Component Correlation analysis.

(2006) BMC Bioinformatics 7

PubMed: 16436213 | PubMedCentral: PMC1386710 | DOI: 10.1186/1471-2105-7-40

However, in a few isolated cases, the difference in the scaled writhing numbers within the same structure set can exceed the threshold of 0.4 that governs similarity (for example, protein pairs (1MAZ,... 2BID), (1F16, 1DDB) in Table 1 , and protein pairs (1C78, 1FM0), (1C78, 1NDD), and (1C78, 1IBQ) in Figure 5(b) .

The atomic coordinates were retrieved from PDB with accession codes 1A4F, 1A6G, 1COL (A), 1DDB (A), 1F16 (A), 1G5M (A), 1GJH (A), 1MAZ, 1MDT (A), and 2BID (A), where (A) means chain A. Set II is also "mainly alpha" and has the same architecture as Set I, including structures 1CK7 (A), 1CXW (A), 1E8B (A), 1E88 (A), 1J7M (A), 1KS0 (A), 1PDC, and 2FN2.

Publication Year: 2006

Conformational changes and protein stability of the pro-apoptotic protein Bax.

(2009) J Bioenerg Biomembr 41

PubMed: 19255832 | PubMedCentral: PMC2778690 | DOI: 10.1007/s10863-009-9202-1

Bax structure was illustrated with Pymol using the PDB file 1F16 of monomeric Bax ( Suzuki et al. 2000 ).

The secondary as well as a cartoon of the ternary structure of Bax (PDB:1F16) are shown in a and b , respectively.

Publication Year: 2009

Translocation of a Bak C-terminus mutant from cytosol to mitochondria to mediate cytochrome C release: implications for Bak and Bax apoptotic function.

(2012) PLoS One 7

PubMed: 22442658 | PubMedCentral: PMC3307716 | DOI: 10.1371/journal.pone.0031510

Images were generated in Pymol using the RCSB Protein Data Bank file 1F16 for Bax [38] .

Publication Year: 2012

Dynamic interaction of cBid with detergents, liposomes and mitochondria.

(2012) PLoS One 7

PubMed: 22540011 | PubMedCentral: PMC3335097 | DOI: 10.1371/journal.pone.0035910

B. Superposition of mouse Bid (colored) and human Bax (black, PDB 1F16).

Publication Year: 2012

Charge profile analysis reveals that activation of pro-apoptotic regulators Bax and Bak relies on charge transfer mediated allosteric regulation.

(2012) PLoS Comput Biol 8

PubMed: 22719244 | PubMedCentral: PMC3375244 | DOI: 10.1371/journal.pcbi.1002565

To this end, we obtained the 3D structure of inactive Bax ( Figure 1B ), and of active Bax in complex with the activator peptide Bim-SAHB ( Figure 1C ) from the Protein Data Bank (PDB IDs 1F16 [16] an... 2K7W [18] respectively).

Publication Year: 2012

Dynamics of Bcl-xL in water and membrane: molecular simulations.

(2013) PLoS One 8

PubMed: 24116174 | PubMedCentral: PMC3792877 | DOI: 10.1371/journal.pone.0076837

The same is true for Bax whose tail is also bound to its hydrophobic binding pocket (PDB ID 1F16 [ 23 ]).

But there are structures of its two homologs Bcl-w and Bax available (PDB IDs 1O0L and 1F16) which show that their C-terminal tails self associate in a pseudo-substrate like fashion; this is consistent with what we see in our simulations.

Publication Year: 2013

On the intrinsic disorder status of the major players in programmed cell death pathways.

(2013) F1000Res 2

PubMed: 24358900 | PubMedCentral: PMC3829196 | DOI: 10.12688/f1000research.2-190.v1

BAX (PDB ID: 1F16); F .

Publication Year: 2013

Structural biology of the intrinsic cell death pathway: what do we know and what is missing?

(2012) Comput Struct Biotechnol J 1

PubMed: 24688636 | PubMedCentral: PMC3962096 | DOI: 10.5936/csbj.201204007

F) Structure of the multi-domain pro-apoptotic protein, Bax (PDB: 1F16).

Publication Year: 2012

Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods.

(2013) BMC Proc 7

PubMed: 24564962 | PubMedCentral: PMC4044902 | DOI: 10.1186/1753-6561-7-S7-S6

Table 1 Protein and PDB ID list of human apoptosis pathway dataset Protein Name PDB ID (_Chain) AIF 1M6I _A AKT1 1UNQ _A 3CQW _A 3O96 _A AKT2 1MRV _A 1O6K _A 1O6L _A 1P6S _A AKT3 2X18 _A APAF1 1CY5 _A... 1Z6T _A 2YGS _A 3IZA _A 3YGS _C BCL-2 2W3L _A 2XA0 _A BCL-XL 2B48 _A 3FDL _A BID 2BID _A 2KBW _B Bax 1F16 _A 2G5B _I 2XA0 _C 3PK1 _B CASP3 1RHQ _A 1RHQ _B 2DKO _A 2DKO _B 2J32 _A CASP6 2WDP _A CASP7 1F1J _A 1I4O _A 1I51 _A 1I51 _B 2QL9 _A 2QL9 _B CASP8 1QTN _A 1QTN _B 2FUN _B 3H11 _B CASP9 1JXQ _A 1NW9 _B 3D9T _C 3YGS _P Calpain1 1ZCM _A Calpain2 1KFU _L 2NQA _A Cn(CHP) 2E30 _A Cn(CHP2) 2BEC _A Cn(PPP3CA) 1AUI _A 1MF8 _A 2R28 _C 3LL8 _A Cn(PPP3R1) 1AUI _B 1MF8 _B 3LL8 _B CytC 1J3S _A DFF40 1IBX _A DFF45 1IBX _B 1IYR _A FADD 1A1W _A 2GF5 _A 3EZQ _B FLIP 3H11 _A Fas 3EWT _E 3EZQ _A IAP(BIRC2) 3D9T _A 3M1D _A 3MUP _A IAP(BIRC3) 2UVL _A 3EB5 _A 3EB6 _A 3M0A _D 3M0D _D IAP(BIRC4) 1G73 _C 1I4O _C 1I51 _E 1NW9 _A 2ECG _A 2KNA _A 2POI _A 3CM7 _C IκBα 1IKN _D 1NFI _E IKK 2JVX _A 3BRT _B 3BRV _B 3CL3 _D 3FX0 _A IL-1(A) 2ILA _A IL-1(B) 1ITB _A 2NVH _A 3O4O _A IL-1R(1) 1ITB _B IL-1R(RAP) 3O4O _B IL-3 1JLI _A IL-3R 1EGJ _A IRAK2 3MOP _K IRAK4 2NRU _A 3MOP _G MyD88 2JS7 _A 3MOP _A NF-κB(NFKB1) 1IKN _C 1NFI _B 1SVC _P 2DBF _A NF-κB(RELA) 1IKN _A 1NFI _A NGF 1WWW _V 2IFG _E PI3K(PIK3CA) 2ENQ _A 2V1Y _A 3HHM _A PI3K(PIK3CG) 1E8Y _A PI3K(PIK3R1) 1A0N _A 1H9O _A 1PBW _A 2IUG _A 2V1Y _B 3HHM _B 3I5R _A PI3K(PIK3R2) 2KT1 _A 2XS6 _A 3MTT _A PRKACA 3AGM _A PRKAR2A 2IZX _A TNFα 1A8M _A 4TSV _A TNF-R1 1EXT _A 1ICH _A TP53 1AIE _A 1OLG _A 1XQH _B 1YC5 _B 2B3G _B 2FOO _B 2GS0 _B 2K8F _B 2VUK _A 3D06 _A 3DAB _B 3LW1 _P TRADD 1F3V _A TRAF2 1CZZ _A 1D00 _A 1F3V _B 3KNV _A 3M0A _A 3M0D _A TRAIL 1D4V _B 1DG6 _A 1DU3 _D TRAIL-R 1D4V _A 1DU3 _A TrkA 1HE7 _A 1SHC _B 1WWW _X 2IFG _A The abbreviations used are: AIF, apoptosis-inducing factor, mitochondrion-associated, 1 (AIFM1); AKT1, RAC-alpha serine/threonine-protein kinase; AKT2, RAC-beta serine/threonine-protein kinase; AKT3, RAC-gamma serine/threonine-protein kinase; APAF1, apoptotic peptidase activating factor 1; BCL-2, B-cell lymphoma 2; BCL-XL, BCL extra-large; BID, BH3 interacting domain death agonist; Bax, BCL-2-associated × protein; CASP3/6/7/8/9, caspase-3/6/7/8/9; Cn(CHP), calcineurin B homologous protein 1; Cn(CHP2), calcineurin B homologous protein 2; Cn(PPP3CA), protein phosphatase 3 catalytic subunit alpha isoform; Cn(PPP3R1), protein phosphatase 3 regulatory subunit 1; CytC, cytochrome C; DFF40, DNA fragmentation factor, 40kDa, beta polypeptide; DFF45, DNA fragmentation factor, 45kDa, alpha polypeptide; FADD, Fas-associated via death domain; FLIP, FLICE/CASP8 inhibitory protein (CASP8 and FADD-like apoptosis regulator, CFLAR); Fas, tumor necrosis factor receptor (TNF) superfamily member 6; IAP, inhibitor of apoptosis; BIRC2/3/4, baculoviral IAP repeat-containing protein 2/3/4; IκBα, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor alpha; IKK, inhibitor of nuclear factor kappa-B kinase; IL-1(A), interleukin-1 alpha; IL-1(B), interleukin-1 beta; IL-1R(1), type 1 interleukin-1 receptor; IL-1R(RAP), interleukin-1 receptor accessory protein; IL-3, interleukin-3; IL-3R, interleukin-3 receptor; IRAK2/4, interleukin-1 receptor-associated kinase 2/4; MyD88, myeloid differentiation primary response protein MyD88; NF-κB(NFKB1), nuclear factor of kappa light polypeptide gene enhancer in B-cells; NF-κB(RELA), nuclear factor of kappa light polypeptide gene enhancer in B-cells 3; NGF, nerve growth factor (beta polypeptide); PI3K, phosphatidylinositide 3-kinase; PIK3CA, PI3K subunit alpha; PIK3CG, PI3K subunit gamma; PIK3R1, PI3K regulatory subunit alpha; PIK3R2, PI3K regulatory subunit beta; PRKACA, cyclic adenosine monophosphate (cAMP)-dependent protein kinase catalytic subunit alpha; PRKAR2A, cAMP-dependent protein kinase type II-alpha regulatory subunit; TNFα, tumor necrosis factor; TNF-R1, TNF receptor superfamily member 1A; TP53, cellular tumor antigen p53; TRADD, TNF receptor type 1-associated death domain protein; TRAF2, TNF receptor-associated factor 2; TRAIL, TNF receptor superfamily member 10; TRAIL-R, TNF receptor superfamily member 10B; TrkA, neurotrophic tyrosine kinase receptor type 1.

Publication Year: 2013

Small-molecule Bax agonists for cancer therapy.

(2014) Nat Commun 5

PubMed: 25230299 | PubMedCentral: PMC4172359 | DOI: 10.1038/ncomms5935

Our computational screen was directed toward the solution structure of Bax (PDB ID: 1F16) 12 .

We analyzed the 3-D solution structure of Bax protein (PDB ID: 1F16) using the UCSF DOCK 6.0 program suite as previously described 13 , 19 .

Publication Year: 2014

Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach.

(2014) Genome Med 6

PubMed: 25360158 | PubMedCentral: PMC4213513 | DOI: 10.1186/s13073-014-0081-7

The BAX gene had the highest number of cancer cell line mutations in the pocket regions (PDB ID: 1F16).

Publication Year: 2014

Galectin-3 leads to attenuation of apoptosis through Bax heterodimerization in human thyroid carcinoma cells.

(2014) Oncotarget 5

PubMed: 25393982 | PubMedCentral: PMC4259453 | DOI: null

In silico docking analysis We used Second ClusPro 2.0 server ( ) to perform rigid-body docking of Gal-3 CRD (1A3K) with Bax (1F16) from RCSB PDB ( b/ ).

Publication Year: 2014