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PDB ID Mentions in PubMed Central Article count: 8

Citations in PubMed

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PDB ID Mentions in PubMed Central

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DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies.

(2007) PLoS Comput Biol 3

PubMed: 17397256 | PubMedCentral: PMC1848003 | DOI: 10.1371/journal.pcbi.0030061

Accession Numbers The structures we used in Figure 8 have the following Protein Data Bank ( http://www.pdb.org ) accession numbers: 9ANT, 2EZD, 1HRY, 1IF1, 1DH3, 1BC8, 2NLL, 1H88, 1PDN, 1SVC, 1SRS, 1M... Y, 1AN2.

Publication Year: 2007


Analysis of the impact of solvent on contacts prediction in proteins.

(2009) BMC Struct Biol 9

PubMed: 19368710 | PubMedCentral: PMC2676287 | DOI: 10.1186/1472-6807-9-22

Interacting partners PFAM ID1/ID2 PDB ID a N b % iden c L 1 d L 2 e X d dry f Opt Xd α g X d wet | opt α h Tyrosine kinase SH3/SH2 domains PF00018/PF00017 2SRC 19 35 57 83 1.86 0.2 3.2... Alcohol dehydrogenase N-/C-domains PF08240/PF00107 1ADG 89 23 128 143 3.52 0.2 3.64 Mg superoxide dismutase N-/C-domains PF00081/PF02777 1AP5 23 44 82 107 4.76 0.2 5.04 Immunoglobulin heavy/light chains PF00047/PF00047 12E8 116 36 107 114 13.56 0 13.56 Ortnithine transferase N-/C-domains PF02729/PF00185 1DUV 20 30 142 178 4.47 0.1 4.94 NFKB factor RHD/TIG domains PF00554/PF01833 1SVC 21 40 199 100 4.56 0.5 4.62 STAT alpha/binding domains PF01017/PF02864 1BF5 32 38 180 251 4.30 0.2 4.42 Mur-ligase catalytic/C-terminal domains PF01225/PF08245 1E8C 26 25 82 208 1.84 0.1 2.12 Dynamin central/N-domains PF00350/PF01031 2AKA 32 40 174 89 0.04 0.2 0.14 Trk C-/N-domains PF02254/PF02080 1LNQ 42 20 114 72 0.53 1 0.78 a PDB ID of the reference structure; b Number of sequences in the multiple sequence alignment; c Average percentage of sequences pairwise similarity; d, e Lengths of the reference sequences; f Values for α = 0; g α value corresponding to the highest X d ; h X d highest value.

Publication Year: 2009


Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

(2012) BMC Bioinformatics 13

PubMed: 22800292 | PubMedCentral: PMC3472317 | DOI: 10.1186/1471-2105-13-165

Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing Group Families Representative(s) HTH &#... 000a0;     Cro & repressor 1LMB   Homeodomain 1FJL, 1HDD, 6PAX   LacI repressor 1WET   Endonuclease Fok1 1FOK   Gamma Delta resolvase 1GDT   Hin recombinase 1HCR   RAP1 family 1IGN   Prd paired domain 1PDN   Tc3 transposase 1TC3   Trp repressor 1TRR   Diptheria tox repressor 1DDN   Transcription factor IIB 1D3U   Interferon regulatory 2IRF   Catabolite gene activator protein 1RUO   Transcription factor 1CF7, 3HTS   Ets domain 1BC8 Zinc Co-ordinating       β-β-α zinc finger 1ZAA   Harmone Nuclear Receptor 2NLL   Loop sheet helix 1TSR   GAL4 type 1ZME Zipper type       Leucine Zipper 1YSA   Helix loop helix 1AN2 Other-α Helix       Pappilomavirus 1 E2 2BOP   Histone 1AOI   EBNA1 nuclear protein 1B3T   Skn-1 transcription factor 1SKN   Cre Recombinase 1CRX   High Mobility Group 1QRV   MADS box 1MNM β-Sheet       TATA box binding 1YTB β-Hairpin/Ribbon       MetJ repressor 1CMA   Tus replication terminator 1ECR   Integration host factor 1IHF   Transcription Factor T-domain 1XBR   Hyperthermophile DNA 1AZP   Arc repressor 1PAR Other       ReI homology 1SVC   Stat protein 1BF5 Enzyme       Methyltransferase 6MHT   Endonuclease PvuII 3PVI   Endonuclease ecorV 1RVA   Endonuclease ecorI 1QPS   Endonuclease BamHI 3BAM   Enonuclease V 1VAS   Dnase I 2DNJ   DNA mismatch endonuclease 1CW0   DNA polymerase β 1BPY   DNA Polymerase I 2BDP   DNA Polymerase T7 1T7P,1CLQ   HIV Reverse Transcriptase 2HMI   Uracil DNA glycosylase 1SSP   3-Methyladenine DNA glycosylase 1BNK   Homing endonuclease 1A73, 1BP7   TopoisomeraseI 1A31 For all the 59 selected representatives, PSI-BLAST profiles were again built against dummy database using the earlier profile creation parameters (as described in Methods).

Publication Year: 2012


Dietary phytochemicals as potent chemotherapeutic agents against breast cancer: Inhibition of NF-?B pathway via molecular interactions in rel homology domain of its precursor protein p105.

(2013) Pharmacogn Mag 9

PubMed: 23661994 | PubMedCentral: PMC3647395 | DOI: 10.4103/0973-1296.108140

Figure 1 Chemical structure of dietary phytochemicals (a) Boswellic Acid (b) 1-Caffeoylquinic acid (c) Ellagic Acid (d) Emodin (e) Genistein (f) Guggulsterone (g) Quercetin (h) Resveratrol (i) Sylibin... n MATERIALS AND METHODS Retrieval of protein 3D structure The crystal structure of NF-κB (PDB: 1SVC) taken in this study was extracted from Brookhaven Protein Data Bank ( http://www.rcsb.org/pdb ).

Publication Year: 2013


?-Keto esters from ketones and ethyl chloroformate: a rapid, general, efficient synthesis of pyrazolones and their antimicrobial, in silico and in vitro cytotoxicity studies.

(2013) Org Med Chem Lett 3

PubMed: 23870758 | PubMedCentral: PMC3726461 | DOI: 10.1186/2191-2858-3-6

The PDB entry 1SVC (pancreatic cancer), 3B8Q (renal cancer) and 4FLH (colon cancer) were selected for structural analysis based on its high-resolution crystallographic structure.

We selected nuclear factor kappa b (NF-κb), vascular endothelial growth factor receptor-2 and human phosphoinositide 3-kinase (PI3K-gamma) (PDB ID: 1SVC, 3B8Q and 4FLH, respectively) as target proteins to carry out the docking analysis of our synthesized compounds.

Publication Year: 2013


The velvet family of fungal regulators contains a DNA-binding domain structurally similar to NF-?B.

(2013) PLoS Biol 11

PubMed: 24391470 | PubMedCentral: PMC3876986 | DOI: 10.1371/journal.pbio.1001750

Figure S12 Superposition-based modelling of DNA (from the NFκB complex structure PDB ID code 1SVC) on the VosA 1–190 homodimer (A, B) and VosA 1–190 -VelB heterodimer (C, D) an... its spatial arrangement.

VosA Residues Involved in DNA-Binding Utilizing the structural similarity to NF-κB, the mode of DNA binding of the velvet domain may be deduced from the superposition of the VosA monomer to crystal structures of NF-κB-DNA complexes [25] , [26] —for example, the NF-κB p50 homodimer bound to DNA (PDB ID code 1SVC).

This strongly indicates that this loop of VosA is involved in protein–DNA interactions, which is consistent with structural superposition with the NF-κB-DNA complex (PDB ID code 1SVC) ( Figure 3C,D ).

Figure S8 Structure-based sequence alignment of the crystallized VosA fragment with NFκB (PDB ID code 1SVC) and VelB reveals a high structural similarity in the canonical fold region but differences in loop regions and the C-terminal region.

(C) Structure-based sequence alignment of VosA (top) and NF-κB (PDB ID code 1SVC; bottom).

Publication Year: 2013


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


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4346863

The p50-DNA (PDB ID: 1SVC) and p65-DNA (PDB ID: 2RAM) homodimer complexes were downloaded from the PDB database.

Publication Year: 2015