Citations in PubMed

Primary Citation PubMed: 16141317 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

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 knowledge-driven approach for crystallographic protein model completion.

(2008) Acta Crystallogr D Biol Crystallogr 64

PubMed: 18391408 | PubMedCentral: PMC2467521 | DOI: 10.1107/S0907444908001558

Protein R (Å) f C r C ( L ) r ( L ) t (s) 2abb 1.0 361 7 334 1 356 51 2jae 1.3 955 17 909 6 929 18 1i12 1.3 619 8 579 6 585 16 1wpn 1.3 374 16 312 8 342 84 1zua 1.3 317 11 260 1 307 30 2 a 50 ... .3 457 21 386 8 425 131 2nw8 1.6 534 8 495 7 497 141 1fgo 1.6 817 22 731 3 791 53 1h5a 1.6 306 13 259 1 303 29 1ou8 1.6 231 5 215 4 217 14 1tm7 1.6 345 4 303 2 333 102 2b3k 1.6 304 5 287 2 294 94 2b9h 1.6 349 5 329 3 334 66 1j4a 1.9 1325 19 1171 12 1188 72 2fsa 1.9 507 6 481 3 492 37 2ij3 1.9 907 17 842 5 885 20 2aka 1.9 1069 17 931 7 966 74 1oim 2.2 887 12 852 3 868 40 2 aa 5 2.2 510 7 485 4 491 309 1zrq 2.2 836 17 753 12 767 88 1vg0 2.2 663 9 640 5 650 126 1e8h 2.6 1090 25 1002 10 1029 42 1o70 2.6 296 5 279 1 292 81 2arh 2.6 584 16 503 9 520 13 2bvm 2.6 541 8 504 2 520 50 1gmo 3.0 1369 73 820 67 828 242 2bxr 3.0 890 40 590 21 604 96 1b9x 3.0 577 16 444 8 460 28 1r5o 3.0 409 16 258 6 273 31 1yhn 3.0 248 7 186 4 193 7 1zy1 3.0 388 18 292 8 321 16 2a2z 3.0 885 31 742 21 754 235 2deo 3.0 399 12 310 10 313 63 1s78 3.3 1995 72 952 39 974 232 1j1e 3.3 720 14 164 14 164 99 2dcu 3.3 544 24 293 13 312 11 2ffl 3.3 2896 105 1839 76 1844 126

Publication Year: 2008


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


Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model.

(2009) BMC Struct Biol 9

PubMed: 19591676 | PubMedCentral: PMC2719638 | DOI: 10.1186/1472-6807-9-45

a. myosin We have examined the large conformational change (see Figure 2d ) from a pre-powerstroke transition-state structure (PDB: 1VOM ) to a post-powerstroke nucleotide-free structure (PDB: 2AKA ),... which pertains to the force generation and hydrolysis product release in myosin [ 81 ].

Also shown in panel (d) is the observed conformational change from a pre-powerstroke myosin structure (PDB: 1VOM , colored in silver) to a post-powerstroke myosin structure (PDB: 2AKA , colored in cyan) superimposed along the N-terminal subdomain (residues 80–186), including rotations of U50, L50 and converter subdomains (shown as arrows).

Publication Year: 2009


Coassembly of Mgm1 isoforms requires cardiolipin and mediates mitochondrial inner membrane fusion.

(2009) J Cell Biol 186

PubMed: 19752025 | PubMedCentral: PMC2753158 | DOI: 10.1083/jcb.200906098

1JWY , 2AKA , and 2J69 ) as references.

1JWY , 2AKA , and 2J69 ).

Publication Year: 2009


G domain dimerization controls dynamin's assembly-stimulated GTPase activity.

(2010) Nature 465

PubMed: 20428113 | PubMedCentral: PMC2879890 | DOI: 10.1038/nature09032

Fig. 3 Active site conformational changes induced by dynamin G-domain dimerization and GTP hydrolysis a, A monomer from the GG dimer structure (green) is superimposed with the nucleotide free rat dyna... in G domain structure (magenta, PDB: 2aka).

d–f, Conformational changes of the dynamin specific loop (colored blue) are mediated by a dense network of hydrogen bonding that includes switch I residues (red), as shown for d, nucleotide free rat dynamin GTPase domain (c, PDB: 2aka); e, GDP.AlF4--stabilized GG dimer (d, long axis crystal form), and f, GDP-bound Dictyostelium dynamin A (e, PDB: 1jwy).

Superposition shows a monomer from the GG dimer structure (green) superimposed with the nucleotide free rat dynamin G domain structure (PDB: 2aka, magenta).

G domain conformational changes promote stimulated-hydrolysis Superposition of GG with the rat dynamin GTPase domain (PDB: 2aka) reveals a number of significant conformational changes in the active site that prime dynamin for GTP hydrolysis ( Fig. 3a ).

Publication Year: 2010


Structural basis for the allosteric interference of myosin function by reactive thiol region mutations G680A and G680V.

(2011) J Biol Chem 286

PubMed: 21841195 | PubMedCentral: PMC3186370 | DOI: 10.1074/jbc.M111.265298

Both apo state motor domain structures are very similar to each other but differ greatly from the previously published structure of the nucleotide-free D. discoideum wild-type motor domain (PDB ID 2AK... ( 29 )) as well as from other apo-state wild-type myosins of class 2 (PDB IDs 3I5G , 3I5H , 2EC6 , 3I5H , 3I5G , and 2OS8 ( 30 )) and class 5 (PDB IDs 1OE9 ( 31 ) and 1W8J ( 32 )).

A , shown is an overview of the G680A apo motor domain structure ( green ) superimposed on the wild-type myosin-2 x-ray structure in the apo state ( yellow , PDB ID 2AKA ).

For the simulations of the wild type, coordinates of the Dd myosin-2 motor domain in the rigor state were used (PDB ID 2AKA ).

Publication Year: 2011