Citations in PubMed

Primary Citation PubMed: 10639123 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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A Caenorhabditis elegans wild type defies the temperature-size rule owing to a single nucleotide polymorphism in tra-3.

(2007) PLoS Genet 3

PubMed: 17335351 | PubMedCentral: PMC1808073 | DOI: 10.1371/journal.pgen.0030034

For the “open” configuration the best match is with human M-calpain (pdb code—1kfu) with an E-value of 0.000686, 36.5% identity, and 67.5% similarity.

Publication Year: 2007

Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.

(2009) Adv Appl Bioinform Chem 2

PubMed: 21918618 | PubMedCentral: PMC3169947 | DOI: null

Supplementary data Table S1 Heterodimer entries not used to construct the scoring functions PDBID a Chain 1 Chain 2 Residue 1 b Residue 2 c 1b0n A B 111 57 1dce C D 567 331 1dev C D 196 41 1e44 B A 96... 85 1euc B A 396 311 1euv A B 211 86 1f2t A B 149 148 1f34 A B 326 149 1f3u F E 171 118 1f60 A B 458 94 1fs0 G E 230 138 1g8k F E 825 133 1gk9 B A 557 260 1go3 M N 187 107 1gzs A B 180 165 1h0h A B 977 214 1h1r A B 303 258 1h9h * E I 223 36 1hfe M T 421 123 1i2m B A 402 216 1izn A B 286 277 1jdh A B 529 38 1jkg B A 250 140 1jlt A B 122 122 1ka9 F H 252 200 1kfu L S 699 184 1ld8 B A 437 382 1lp1 A B 58 58 1m1e A B 538 81 1mtp A B 323 43 1mu2 A B 555 426 1n1j B A 97 93 1nf3 A C 195 128 1o94 D C 320 264 1o97 D C 320 264 1oo0 A B 147 110 1or7 B F 194 90 1p5v A B 235 147 1q7l A B 198 88 1r8o A B 96 71 1rp3 G H 239 88 1s9d E A 203 164 1tqy G H 424 415 1ubk L S 534 267 1ugp B A 226 203 1vet B A 125 124 1vf6 B D 83 72 6req C D 727 637 Notes: a The entry with * 1h9h, failed in the energy minimization.

Publication Year: 2009

Calpain-5 mutations cause autoimmune uveitis, retinal neovascularization, and photoreceptor degeneration.

(2012) PLoS Genet 8

PubMed: 23055945 | PubMedCentral: PMC3464205 | DOI: 10.1371/journal.pgen.1003001

Yasara Structure (version 11.3.2) was used to generate a homology model of human calpain-5 using calpain-2 (m-calpain) structures (pdb id: 3BOW, 1DF0, 1U5I, 1KFU) as templates [12] , [13] .

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

Homology modeling study of bovine ?-calpain inhibitor-binding domains.

(2014) Int J Mol Sci 15

PubMed: 24806345 | PubMedCentral: PMC4057710 | DOI: 10.3390/ijms15057897

To these were added some other reference proteins known as active CAPN structures (PDB code 1KFU:L, 1KFX:L, 1DF0:A, 1U5I:A, and 3DF0:A in Table 4 ) with their whole sequence or their protease core reg... ons ( Figure 4 ).

PDB ID Molecular description Experimental details Length Sequence identity (%) Sequence similarity (%) E -value Template 1QXP:B Like CAPN1 (rat) X-ray Diffraction (2.80 Å) 788 74.6 82.4 0.0 T 1KXR:B Ca 2+ bound protease core of CAPN1 (rat) X-ray Diffraction (2.07 Å) 321 80.2 85.8 1 × 10 −17 T 3BOW:A CAPN2 catalytic subunit (rat) X-ray Diffraction (2.40 Å) 680 59.4 77 0.0 T 3BOW:C CAST 4 domain (rat) X-ray Diffraction (2.40 Å) 65 72.9 86.4 3 × 10 −10 T 1KFX:L Form I of CAPN2 (human) X-ray Diffraction (3.15 Å) 640 57.1 75.7 0.0 - 1KFU:L Form II of CAPN2 (human) X-ray Diffraction (2.50 Å) 699 61.4 81.3 0.0 - 3DF0:A CAPN2 catalytic subunit (rat) X-ray Diffraction (2.95 Å) 676 59.5 77.5 0.0 - 1U5I:A CAPN2 mutant Lys10Thr (rat) X-ray Diffraction (2.86 Å) 625 56.1 73.4 0.0 - Table 5.

Publication Year: 2014