Cytochrome P450 HomepageNelson, DR (2009) The Cytochrome P450 Homepage. Human Genomics 4, 59-65.AlphafoldJohn Jumper, Richard Evans, Alexander Pritzel, et al. - Highly accurate protein structure prediction with AlphaFold. Nature, 1–11, doi: 10.1038/s41586-021-03819-2 (2021)ColabfoldMirdita M, Ovchinnikov S and Steinegger M. ColabFold - Making protein folding accessible to all. bioRxiv, doi: 10.1101/2021.08.15.456425 (2021)Localcolabfoldhttps://github.com/YoshitakaMo/localcolabfoldTM-score on-line for GDT-TS Scorehttps://zhanggroup.org/TM-score/Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins, 57: 702-710 (2004). J. Xu, Y. Zhang, How significant is a protein structure similarity with TM-score=0.5? Bioinformatics, 26, 889-895 (2010).TM-align on-line (Version 20190822)https://zhanggroup.org/TM-score/Y. Zhang, J. Skolnick, TM-align: A protein structure alignment algorithm based on TM-score, Nucleic Acids Research, 33: 2302-2309 (2005)Local-Global Alignment (provided by Adam Zemla) for GDT-TS Scorehttp://linum.proteinmodel.org/AS2TS/LGA/lga.htmlZemla A., "LGA - a Method for Finding 3D Similarities in Protein Structures", Nucleic Acids Research, 2003, Vol. 31, No. 13, pp. 3370-3374.https://proteopedia.org/wiki/index.php/Calculating_GDT_TS
101A1_m5 vs 2ZWU 0.9911101D1_m5 vs 4C9M 0.9931102A1_m5 vs 2IJ2 0.9857105A1_m3 vs 2ZBX 0.9734107A1_m5 vs 1Z8O0.9404108A1_m3 vs 1CPT 0.9736113A1_m3 vs 2JJN 0.9532119A1_m4 vs 1IO7 0.9865120A1_m3 vs 2VE3 0.9777121A1_m5 vs 1N40 0.9887125A1_m2 vs 2X5W 0.9832126A1_m5 vs 5LI8 0.9483130A1_m2 vs 2WHF 0.9876134A1_m1 vs 3NC3 0.9580142A1_m2 vs2XKR 0.9830144A1_m3 vs 5HDI 0.9002152A1_m3 vs1IZO0.9928154A1_m1vs 1ODO0.9785
Cα RMSD
101A1_m5 vs 2ZWU 0.70101D1_m5 vs 4C9M 0.61102A1_m5 vs 2IJ2 0.94105A1_m3 vs 2ZBX 0.90107A1_m5 vs 1Z8O2.06108A1_m3 vs 1CPT 1.39113A1_m3 vs 2JJN 1.48119A1_m4 vs 1IO7 0.90120A1_m3 vs 2VE3 1.18121A1_m5 vs 1N40 0.86125A1_m2 vs 2X5W 1.13126A1_m5 vs 5LI8 1.97130A1_m2 vs 2WHF 0.86134A1_m1 vs 3NC3 1.80142A1_m2 vs2XKR 0.98144A1_m3 vs 5HDI 1.02152A1_m3 vs 1IZO 0.63154A1_m1 vs 1ODO 0.88
GDT-TS Score LGA
101A1_m5 vs 2ZWU97.593%101D1_m5 vs 4C9M 98.836%102A1_m5 vs 2IJ293.444%105A1_m3 vs 2ZBX 96.995%107A1_m5 vs 1Z8O89.046%108A1_m3 vs 1CPT 96.588%113A1_m3 vs 2JJN 94.699%119A1_m4 vs 1IO7 97.603%120A1_m3 vs 2VE3 92.224%121A1_m5 vs 1N40 97.704%125A1_m2 vs 2X5W 97.346%126A1_m5 vs 5LI8 95.620%130A1_m2 vs 2WHF 95.620%134A1_m1 vs 3NC3 91.307%142A1_m2 vs2XKR 94.620%144A1_m3 vs 5HDI 94.192%152A1_m3 vs 1IZO 97.871%154A1_m1 vs 1ODO 93.798%
Structures
CYPsA1familiesMutantCYP10145+245 (D1)49+4CYP10245-33(1aa)CYP1051185CYP107… Under Construction
Alphafold result (localcolabfold using AF2 parameters)spectrum b, rainbow_rev, maximum=100, minimum=502ZWU rotated & Center using F351, C358, G360White
Alphafold result (localcolabfold using AF2 parameters)spectrum b, rainbow_rev, maximum=100, minimum=502ZWU rotated & Center using F351, C358, G360White
TM-Align (model5 vs 2ZWU)Length of Chain_1: 415 residuesLength of Chain_2: 405 residues Aligned length= 405, RMSD= 0.70, Seq_ID=n_identical/n_aligned= 1.000 TM-score= 0.96739 (if normalized by length of Chain_1)TM-score= 0.99110 (if normalized by length of Chain_2)
Alphafold result (localcolabfold using AF2 parameters)spectrum b, rainbow_rev, maximum=100, minimum=504C9M rotated & Center using F358, C365, G367White
TM-Align (model5 vs 4c9m)Length of Chain_1: 421 residuesLength of Chain_2: 408 residues Aligned length= 408, RMSD= 0.61, Seq_ID=n_identical/n_aligned= 1.000 TM-score= 0.96265 (if normalized by length of Chain_1)TM-score= 0.99314 (if normalized by length of Chain_2)
TM-Score (model5 vs 2IJ2)Length of Chain_1: 460 residuesLength of Chain_2: 450 residues Aligned length= 450, RMSD= 0.94, Seq_ID=n_identical/n_aligned= 1.000 TM-score= 0.96450 (if normalized by length of Chain_1)TM-score= 0.98568 (if normalized by length of Chain_2)
TM-Align (model3 vs 2ZBX)Length of Chain_1: 406 residuesLength of Chain_2: 399 residues Aligned length= 393, RMSD= 0.90, Seq_ID=n_identical/n_aligned= 0.995 TM-score= 0.95673 (if normalized by length of Chain_1)TM-score= 0.97337 (if normalized by length of Chain_2)
TM-Align (model5 vs 1Z8O)Length of Chain_1: 406 residuesLength of Chain_2: 402 residues Aligned length= 401, RMSD= 2.06, Seq_ID=n_identical/n_aligned= 0.998 TM-score= 0.94042 (if normalized by length of Chain_1)TM-score= 0.94949 (if normalized by length of Chain_2)
TM-Align (model3 vs 1CPT)Length of Chain_1: 428 residuesLength of Chain_2: 412 residues Aligned length= 411, RMSD= 1.39, Seq_ID=n_identical/n_aligned= 0.995 TM-score= 0.93776 (if normalized by length of Chain_1)TM-score= 0.97361 (if normalized by length of Chain_2)
TM-Align (model3 vs 2JJN)Aligned length= 389, RMSD= 1.48, Seq_ID=n_identical/n_aligned= 0.977 TM-score= 0.95327 (if normalized by length of Chain_1)TM-score= 0.95801 (if normalized by length of Chain_2)
TM-Score (model4 vs 1IO7)Length of Chain_1: 368 residuesLength of Chain_2: 366 residues Aligned length= 366, RMSD= 0.90, Seq_ID=n_identical/n_aligned= 1.000 TM-score= 0.98120 (if normalized by length of Chain_1)TM-score= 0.98651 (if normalized by length of Chain_2)
TM-Align (model3 vs 2VE3)Length of Chain_1: 444 residuesLength of Chain_2: 435 residues Aligned length= 435, RMSD= 1.18, Seq_ID=n_identical/n_aligned= 1.000 TM-score= 0.95820 (if normalized by length of Chain_1)TM-score= 0.97768 (if normalized by length of Chain_2)
TM-Align (model5 vs 1N40)Length of Chain_1: 396 residuesLength of Chain_2: 394 residues Aligned length= 394, RMSD= 0.86, Seq_ID=n_identical/n_aligned= 0.997 TM-score= 0.98373 (if normalized by length of Chain_1)TM-score= 0.98868 (if normalized by length of Chain_2)
TM-Align (model2 vs 6T0H)Length of Chain_1: 425 residuesLength of Chain_2: 430 residues Aligned length= 424, RMSD= 0.86, Seq_ID=n_identical/n_aligned= 0.745 TM-score= 0.98507 (if normalized by length of Chain_1)TM-score= 0.97373 (if normalized by length of Chain_2)
TM-Align (model2 vs 2X5W)Length of Chain_1: 433 residuesLength of Chain_2: 409 residues Aligned length= 409, RMSD= 1.13, Seq_ID=n_identical/n_aligned= 1.000 TM-score= 0.92925 (if normalized by length of Chain_1)TM-score= 0.98315 (if normalized by length of Chain_2)
TM-Align (model5 vs 5LI8)Length of Chain_1: 414 residuesLength of Chain_2: 390 residues Aligned length= 384, RMSD= 1.97, Seq_ID=n_identical/n_aligned= 0.979 TM-score= 0.89437 (if normalized by length of Chain_1)TM-score= 0.94832 (if normalized by length of Chain_2)
TM-Align (model2 vs 2WHF)Length of Chain_1: 405 residuesLength of Chain_2: 394 residues Aligned length= 394, RMSD= 0.86, Seq_ID=n_identical/n_aligned= 0.995 TM-score= 0.96103 (if normalized by length of Chain_1)TM-score= 0.98760 (if normalized by length of Chain_2)
TM-Align (model1 vs 3NC3)Length of Chain_1: 405 residuesLength of Chain_2: 380 residues Aligned length= 378, RMSD= 1.80, Seq_ID=n_identical/n_aligned= 0.950 TM-score= 0.90021 (if normalized by length of Chain_1)TM-score= 0.95801 (if normalized by length of Chain_2)
TM-Align (model2 vs 2XKR)Length of Chain_1: 398 residuesLength of Chain_2: 395 residues Aligned length= 395, RMSD= 0.98, Seq_ID=n_identical/n_aligned= 1.000 TM-score= 0.97567 (if normalized by length of Chain_1)TM-score= 0.98298 (if normalized by length of Chain_2)
TM-Align (model3 vs 5HDI)Length of Chain_1: 397 residuesLength of Chain_2: 434 residues Aligned length= 397, RMSD= 1.02, Seq_ID=n_identical/n_aligned= 0.997 TM-score= 0.98303 (if normalized by length of Chain_1)TM-score= 0.90024 (if normalized by length of Chain_2)
A1(100%)1ODO1.9Å_414aa CYP154sC1(42%)1GWI2.9Å_WT C2(42%)6L691.5Å_WT7CL72.0Å7CL92.0Å C4(42%)6A7J2.7Å_WT C5(42%)4J6B2.2Å_WT4J6C1.9Å4J6D2.4Å4JBT2.2Å6TO22.0Å Similar to CYP107
Alphafold result (localcolabfold using AF2 parameters)spectrum b, rainbow_rev, maximum=100, minimum=50---- rotated & Center using White