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. 2019 Dec 2;8(12):2117. doi: 10.3390/jcm8122117

Table 1.

List of the investigated homologous crystallized structures and specific structural features. The proteins sampled using pGenTHREADER together with the RMSD between coordinates of the sampled structure backbones superimposed to the structure of the three query sequences (AIF (4bur.pdb); NDI (4g73.pdb); and NDH-2 (5kmr.pdb)) are reported. The best hit of each reported structure sampled by Blastp in H.sapiens, C. thermarum, and S. cerevisiae is also reported. For each best hit E-value, %ID and query coverage are also reported. Abbreviations: AIF, apoptosis-inducing factor; DH, dehydrogenase; LD, lipoamide dehydrogenase; DLD, dihydrolipoyl dehydrogenase or dihydrolipoamide dehydrogenase; OX, oxidase; RED, reductase; GLR1, glutathione disulfide reductase; Trx, Thioredoxin; mt, mitochondrial; TRR1, Trx-disulfide reductase; RYL-552, 5n.a.fluoron.a.3n.a.methyln.a.2n.a.{4n.a.(4n.a.(trifluoromethoxy)benzyl)phenyl}quinolinn.a.4(1H)n.a.one); SL827, N~2~-((2-amino-5-bromopyridin-3-yl)sulfonyl)-N-(4-methoxyphenyl)-N~2~-methylglycinamide; KPC, ketopropylthioethanesulphonate; CytC, Cytochrome C.

Functional Annotation Res. N. Organism Crystallized cofactors Crystallized Inhibitors AIF (4bur) NDH2-(5kmr) NDI (4g73) H. sapiens Blast Hits C. thermarum Blast Best Hit S. cerevisiae S288C Blast Best Hit
RMSD (Å) Protein Name Accession Query cover E-val %ID Protein Name Accession Query cover E-val %ID Protein Name Accession Query cover E-val %ID
AIF-like structures
4bur AIF 511 H.sapines FAD/NADH n.a. 0 3.12 2.22 mt isoform AIF-exB NP_665811.1 100% 0.0 100% n.a. n.a. n.a. n.a. n.a. Irc15p NP_015308 25% 0.98 25.55%
5fs8 AIF 474 H.sapines FAD n.a. 1.06 2.71 1.82 mt isoform AIF NP_004199.1 99% 0 99.61% n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a.
5vn0 NADH OX 449 L.brevis FAD/NADH/O2 n.a. 2.28 2.03 2.18 protein transport protein Sec23A NP_006355.2 100% 0.0 100% CoA-disulfide reductase WP_007505374.1 2% 3 × 10−86 50.00% GTPase-activating protein SEC23 NP_015507.1 98% 0.0 49.80%
1xhc NADH OX /nitrile RED 555 P. furiosus FAD n.a. 1.799 2.443 2.458 AIF 3 isoform 2 NP_001018070.1 73% 9 × 10−20 28.47% CoA-disulfide RED WP_007505374.1 98% 9 × 10−92 35.83% Aif1p NP_014472.1 54% 9 × 10−11 26.36%
2bc0 NADH OX 473 S. pyrogens FAD n.a. 1.53 1.859 1.658 AIF 3 isoform 1 NP_653305.1 67% 2 × 10−18 25.75% CoA-disulfide RED WP_007505374.1 92% 2 × 10−74 31.29% GLR1 NP_015234.1 40% 8 × 10−10 27.09%
2cdu NAD(P)H OX 452 L. sanfrancensis FAD/ADP n.a. 2.226 2.2 2.095 mt isoform AIF NP_004199.1 56% 2 × 10−11 25.46% CoA-disulfide RED WP_007505374.1 96% 3 × 10−74 31.52% GLR1 NP_015234.1 39% 3 × 10−8 27.66%
1nhs NADH PerOX 447 E. fecalis FAD n.a. 1.738 1.932 2.041 AIF 3 isoform 1 NP_653305.1 55% 7 × 10−22 27.17% CoA-disulfide RED WP_007505374.1 98% 9 × 10−92 35.83% GLR1 NP_015234.1 39% 8 × 10−4 22.40%
3lxd Ferredoxin RED 409 E. coli n.a n.a. 1.949 2.842 2.606 AIF 3 isoform 1 NP_653305.1 89% 8 × 10−51 30.24% CoA-disulfide RED WP_007505374.1 80% 6 × 10−26 29.48% GLR1 NP_015234.1 35% 2 × 10−3 24.03%
3fg2 Ferredoxin RED 404 R. palustris FAD n.a. 1.633 2.087 2.340 AIF 3 isoform 1 NP_653305.1 91% 6 × 10−47 29.22% CoA-disulfide RED WP_007505374.1 77% 7 × 10−22 24.15% GLR1 NP_015234.1 32% 4 × 10−3 25.90%
2gqw Ferredoxin RED 401 Pseudomonas sp. KKS102 FAD n.a. 1.986 2.362 2.365 AIF 3 isoform 2 NP_001018070.1 91% 5 × 10−27 28.39% CoA-disulfide RED WP_007505374.1 52% 3 × 10−14 29.78% Irc15p NP_015308.1 24% 6 × 10−3 28.85%
2v3a Rubredoxin RED 381 P. aeruginosa FAD n.a. 2.278 3.067 6.698 AIF 2 NP_001185625.1 61% 3 × 10−3 24% CoA-disulfide RED WP_007505374.1 71% 2 × 10−23 27.02% n.a. n.a. n.a. n.a. n.a.
3klj NADH:rubredoxinoxidoRED 378 C. acetobutylicum FAD n.a. 2.498 2.745 2.335 AIF 3 isoform 2 NP_001018070.1 95% 5 × 10−27 23.41% CoA-disulfide RED WP_007505374.1 89% 1 × 10−21 23.69% mRNA-binding ubiquitin-specific protease UBP3 NP_011078.3 7% 0.77 53.57%
3ef6 Toluene 2,3-Dioxygenase RED 400 P. putida FAD n.a. 1.914 1.979 2.146 AIF 3 isoform 1 NP_653305.1 83% 7 × 10−44 33.14% CoA-disulfide RED WP_007505374.1 43% 9 × 10−15 33.33% Aif1p NP_014472.1 48% 6 × 10−4 25.35%
1q1r Putidaredoxin RED 421 P. putida FAD n.a. 1.581 2.85 3.069 AIF 3 isoform 3 NP_001139760.1 87% 5 × 10−40 28.95% CoA-disulfide RED WP_007505374.1 72% 9 × 10−25 27.74% GLR1 NP_015234.1 38% 2 × 10−4 21.64%
3oc4 Pyridine nucleotide-disulfide oxidoRED 422 E. faecalis FAD n.a. 3.143 2.451 3.207 AIF 3 isoform 1 NP_653305.1 62% 4 × 10−13 25.26% CoA-disulfide RED WP_007505374.1 95% 4 × 10−45 26.53% GLR1 NP_015234.1 51% 1 × 10−5 23.36%
3iwa Pyridine nucleotide-disulphideoxidoRED 397 D. vulgaris n.a. n.a. 2.243 3.06 2.664 AIF 3 isoform 2 NP_001018070.1 68% 8 × 10−24 28.66% CoA-disulfide RED WP_007505374.1 95% 5 × 10−82 33.55% GLR1 NP_015234.1 59% 3 × 10−9 22.49%
3cgb Pyridine Nucleotide Coenzyme A-Disulfide RED 444 B.anthracis FAD/CoA n.a. 2.17 2.37 2.341 glycerol-3-phosphate DH, mt NP_000399.3 10% 0.8 39.58% CoA-disulfide RED WP_007505374.1 91% 5 × 10−137 47.05% Irc15p NP_015308.1 60% 1 × 10−5 23.51%
4fx9 CoA disulfide RED 453 P. horikoshii FAD/CoA n.a. 2.148 2.223 2.488 AIF 3 isoform 1 [Homo sapiens] NP_653305.1 70% 1 × 10−22 27.55% CoA-disulfide RED WP_007505374.1 96% 3 × 10−105 39.28% GLR1 NP_015234.1 64% 2 × 10−12 24.36%
3ics CoA disulfide RED 555 B. anthracis ADP/FAD/CoA n.a. 1.845 1.958 1.98 DLD. mt isoform 4 NP_001276681.1 51% 2 × 10−9 26.46% CoA-disulfide RED WP_007505374.1 75% 3 × 10−83 32.13% thiosulfate sulfurtransferase RDL2 NP_014929.3 10% 1 × 10−3 29.73%
3ntd NADH-dependent persulfide RED 565 S. ioihica FAD/CoA n.a. 1.92 1.95 1.95 AIF mt isoform AIF-exB NP_665811.1 47% 6 × 10−10 28.01% CoA-disulfide RED WP_007505374.1 82% 1 × 10−85 31.57% DLD NP_116635.1 45% 2 × 10−7 25.87%
Type II NADH DH-like structures
5kmr Type II NADH DH 405 C. thermarum FAD/NAD n.a. 3.12 0 1.31 AIF 2 NP_001185625.1 72% 2 × 10−10 25.34% NAD(P)/FAD-dependent oxidoRED WP_007502350.1 98% 0.0 100.00% NADH-ubiquinone RED (H(+)-translocating) NDE1 NP_013865.1 80% 7 × 10−29 28.29%
5n1t FlavoCytC sulfide DH 393 T. paradoxus CytC, COPC, FAD n.a. 2.82 3.33 2.96 n.a. n.a. n.a. n.a. n.a. NAD(P)/FAD-dependent oxidoRED WP_007505419.1 74% 5 × 10−22 26.33% n.a. n.a. n.a. n.a. n.a.
5na1 NADH:quinoneoxidoRED 398 S. aureus FAD n.a. 2.63 0.82 1.39 n.a. n.a. n.a. n.a. n.a. NAD(P)/FAD-dependent oxidoRED WP_007502350.1 97% 3 × 10−130 46.48% nucleoside triphosphate pyrophosphohydrolase HAM1 NP_012603.1 12% 0.59 34.69%
5jwc Type II NADH DH 495 P. falciparum FAD RYL-552 3.88 1.68 0.85 AIF 2 NP_001185625.1 6% 1.7 44.44% NAD(P)/FAD-dependent oxidoRED WP_042685058.1 49% 1 × 10−11 22.68% NADH-UQ RED (H(+)-translocating) NDE1 NP_013865.1 94% 8 × 10−60 30.32%
3hyw Sulfide:quinoneoxidoRED 429 aeolicus FAD/DCQ/H2S n.a. 3.52 2.75 2.86 sulfide:quinoneoxidoRED. mt (Homo sapiens) NP_001258142.1 68% 3 × 10−12 23.70% NAD(P)/FAD-dependent oxidoRED WP_007505419.1 75% 4 × 10−15 22.82% NADH-UQ RED (H(+)-translocating) NDE2 NP_010198.1 55% 1 × 10−9 27.27%
Ndi1 - NADH DH like structures
4g73 Ndi1 - NADH DH 502 S. cerevisiae FAD/NAD/UQ5 n.a. 2.22 1.31 0 n.a. n.a. n.a. n.a. n.a. NAD(P)/FAD-dependent oxidoRED WP_007502350.1 86% 1 × 10−30 25.93% NADH-UQ RED (H(+)-translocating) NDI1 NP_013586.1 97% 0.0 99.80%
5yjw Ndi1 - NADH DH. 454 S. cerevisiae FAD Stigmatellin 2.12 1.32 0.49 n.a. n.a. n.a. n.a. n.a. NAD(P)/FAD-dependent oxidoRED WP_007502350.1 90% 7 × 10−31 25.93% NADH-UQ RED (H(+)-translocating) NDI1 NP_013586.1 100% 0.0 100.00%
Other DH
4m52 LD. 465 M. tubercolosis FAD SL827 4.28 4.341 1.974 DLD. mt isoform 1 NP_000099.2 98% 8 × 10−87 35.82% DLD WP_007503768.1 96% 2 × 10−120 44.81% DLD NP_116635.1 96% 3 × 10−86 37.63%
6aon DLD 473 B. pertussis n.a. n.a. 4.84 2.03 3.76 DLD. mt isoform 1 NP_000099.2 98% 7 × 10−141 46.74% DLD WP_007503768.1 98% 1 × 10−106 40.46% DLD NP_116635.1 97% 3 × 10−143 47.81%
4jq9 DLD 471 E. coli FAD n.a. 3.61 2.168 2.238 DLD. mt isoform 1 NP_000099.2 94% 2 × 10−113 43.61% DLD WP_007505013.1 95% 3 × 10−121 43.74% DLD NP_116635.1 93% 3 × 10−100 40.79%
6awa DLD 475 P. putida FAD/AMP n.a. 3.47 2.6 2.67 DLD. mt isoform 1 NP_000099.2 96% 1 × 10−153 50.43% DLD WP_007505013.1 97% 6 × 10−121 43.19% DLD NP_116635.1 97% 1 × 10−140 46.47%
5j5z DLD 477 H. sapiens FAD n.a. 3.23 2.77 3.13 DLD. mt isoform 1 NP_000099.2 95% 0.0 99.97% DLD WP_007505013.1 92% 2 × 10−108 42.30% DLD NP_116635.1 93% 0.0 57.17%
1zmd DLD 474 H. sapiens FAD/NAD n..a. 3.27 2.83 2.77 DLD. mt isoform 1 (Homo sapiens) NP_000099.2 100% 0.0 99.79% DLD WP_007505013.1 96% 2 × 10−110 42.52% DLD NP_116635.1 98% 0.0 57.59%
5u25 DLD 478 N. gonorrhoeae FAD n.a. 3.68 2.44 2.47 DLD. mt isoform 1 NP_000099.2 75% 7 × 10−98 39.48% DLD WP_007505013.1 77% 2 × 10−112 41.76% DLD NP_116635.1 76% 2 × 10−96 40.17%
3urh DLD 491 R. meliloti FAD n.a. 3.376 2.29 1.732 DLD. mt isoform 1 NP_000099.2 95% 1 × 10−179 55.08% DLD WP_007505013.1 94% 3 × 10−117 42.58% DLD NP_116635.1 94% 2 × 10−163 51.37%
1lvl LD 458 P. putida FAD/NADH n.a. 3.664 2.976 4.089 DLD. mt isoform 1 NP_000099.2 98% 5 × 10−90 38.09% DLD WP_007505013.1 99% 2 × 10−132 43.94% DLD NP_116635.1 98% 1 × 10−81 36.86%
1ebd DLD 455 G. stearothermophilus FAD/Dihydrolipoamide acetyltransferase n.a. 3.22 2.19 3.69 DLD.mt isoform 1 NP_000099.2 98% 3 × 10−119 43.89% DLD WP_007505013.1 99% 0.0 68.65% DLD NP_116635.1 98% 3 × 10−110 43.29%
2yqu LD 455 T. thermophilus FAD n.a. 3.884 3.548 2.97 DLD. mt isoform 1 NP_000099.2 98% 4 × 10−140 46.41% DLD WP_007505013.1 99% 1 × 10−115 43.41% DLD NP_116635.1 99% 2 × 10−143 48.00%
3lad Lipoamide deydrogenase 476 A. vinelandii FAD n.a. 4.442 2.221 2.995 DLD. mt isoform 1 NP_000099.2 96% 3 × 10−150 49.36% DLD WP_007505013.1 98% 3 × 10−121 42.55% DLD NP_116635.1 98% 3 × 10−135 44.61%
2r9z Glutathione amide RED 463 C. gracile FAD n.a. 2.813 2.396 2.046 glutathione RED. mt isoform 1 NP_000628.2 95% 9 × 10−147 48.80% DLD WP_007505013.1 94% 2 × 10−64 30.25% GLR1 NP_015234.1 96% 1 × 10−141 46.12%
6n7f Glutathione RED 451 S. pyogenes Riboflavin/FAD n.a. 3.7 2.74 1.98 glutathione RED. mt isoform 1 NP_000628.2 99% 9 × 10−160 52.48% NAD(P)/FAD-dependent oxidoRED WP_042684715.1 88% 1 × 10−53 29.70% GLR1 NP_015234.1 98% 9 × 10−149 48.70%
5vdn Glutathione RED 449 Y. pestis FAD n.a. 3.73 2.41 2.66 glutathione RED. mt isoform 1 NP_000628.2 96% 1 × 10−161 53.90% DLD WP_007505013.1 95% 5 × 10−61 32.09% GLR1 NP_015234.1 96% 9 × 10−149 50.75%
4j56 Trx RED 504 P. falciparum FAD/Trx n.a. 3.45 3.33 2.01 Trx RED 2. mt isoform 2 NP_001339229.1 91% 6 × 10−146 45.13% DLD WP_007505013.1 89% 3 × 10−31 26.23% GLR1 NP_015234.1 89% 3 × 10−74 33.47%
1xdi Flavoprotein Disulfide RED 499 M. tuberculosis FAD n.a. 4.29 2.975 3.65 DLD. mt isoform 1 NP_000099.2 91% 2 × 10−35 25.49% DLD WP_007503768.1 91% 2 × 10−47 29.12% DLD NP_116635.1 92% 8 × 10−35 26.10%
1mo9 NADPH:2-ketopropyl-coenzyme M oxidoRED/carboxylase (2-KPCC) 523 X. autotrophicus FAD KPC 4.724 2.596 3.091 DLD. mt isoform 1 NP_000099.2 87% 4 × 10−24 22.88% NAD(P)/FAD-dependent oxidoRED WP_042684715.1 69% 2 × 10−30 28.65% DLD NP_116635.1 86% 2 × 10−22 22.13%
4k7z Mercuric RED 467 P. aeruginosa FAD/NADP n.a. 3.807 3.341 3.498 DLD. mt isoform 1 NP_000099.2 97% 2 × 10−54 29.32% DLD WP_007505013.1 94% 3 × 10−71 35.68% DLD NP_116635.1 95% 3× 10−51 29.64%
Outliers
4up3 Trx RED 312 E. histolytica FAD/NADPH n.a. 3.59 3.76 3.76 (F-actin)-monooxygenase MICAL2 isoform f NP_001269597.1 13% 0.2 30.23% Trx-disulfide RED WP_007502507.1 99% 8 × 10−68 37.50% TRR1 NP_010640.1 98% 4 × 10−138 60.83%
5u63 Trx RED 315 H. influenzae FAD/NADP n.a. 2.01 3.06 4.393 DLD. mt isoform 1 NP_000099.2 9% 2.2 48.28% Trx-disulfide RED WP_007502507.1 97% 3 × 10−76 39.43% TRR1 NP_011974.1 99% 7 × 10−101 49.85%
1ps9 2,4-dienoyl-CoA RED 671 E. coli FMN/FAD/NADP n.a. 2.02 3.93 2.16 L-amino-acid OX isoform 2 NP_001244946.1 6% 3.1 40.48% NADPH DH NamA WP_007504681.1 49% 1 × 10−30 30.00% NADPH DH NP_012049.1 34% 3 × 10−19 26.98%