Reference
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-linehttps://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).Reference
D. R. Nelson's
D. R. Nelson's
https://twitter.com/P450nelson/status/1501396401317883904
Method
Localcolabfold (model1_ptm, recycle=6 or CaRMSD < 0.4, centerd and rotated around proximal Cys)runner_P450align.py -f CYPs/CYPXXXA1.fasta -nm 5 -mr 6 -alirunner_P450align.py -f CYPs/CYPXXXA1.fasta -nm 5 -mr 6 -ali -upAlign crystal struvture at FXXXXXXCXGaligin_P450.py -i XXXX.P450 -al1 "residue No. F" -al2 "residue No. G" -al3 "residue No. C"Method
CYP105A
>CYP105A1 ---- 1234567890 1234567890 1234567890 1234567890 1234567890 ----0001 MTDTATTPQT TDAPAFPSNR SCPYQLPDGY AQLRDTPGPL HRVTLYDGRQ 00500051 AWVVTKHEAA RKLLGDPRLS SNRTDDNFPA TSPRFEAVRE SPQAFIGLDP 01000101 PEHGTRRRMT ISEFTVKRIK GMRPEVEEVV HGFLDEMLAA GPTADLVSQF 01500151 ALPVPSMVIC RLLGVPYADH EFFQDASKRL VQSTDAQSAL TARNDLAGYL 02000201 DGLITQFQTE PGAGLVGALV ADQLANGEID REELISTAML LLIAGHETTA 02500251 SMTSLSVITL LDHPEQYAAL RADRSLVPGA VEELLRYLAI ADIAGGRVAT 03000301 ADIEVEGHLI RAGEGVIVVN SIANRDGTVY EDPDALDIHR SARHHLAFGF 03500351 GVHQCLGQNL ARLELEVILN ALMDRVPTLR LAVPVEQLVL RPGTTIQGVN 04000401 ELPVTWCYP105A
Heme Docked
Heme Docked
Alphafold result (localcolabfold using AF2 parameters)spectrum b, rainbow_rev, maximum=100, minimum=502ZBX rotate & Center by F348, C355, G357White
TM-alignmodel3 in thick and 2ZBX in thin wirefamesResidues with d<5A in red
TM-Score (model3 vs 2ZBX)Number of residues in common= 395
RMSD of the common residues= 1.485 TM-score = 0.9740 (d0= 7.21) MaxSub-score= 0.9450 (d0= 3.50)
GDT-TS-score= 0.9530 %(d<1)=0.8797 %(d<2)=0.9649 %(d<4)=0.9825 %(d<8)=0.9850 %
GDT-HA-score= 0.8584 %(d<0.5)=0.6065 %(d<1)=0.8797 %(d<2)=0.9649 %(d<4)=0.9825 %
https://zhanggroup.org/TM-score/tmp/578688.html
TM-Score (model3 vs 2ZBX)Number of residues in common= 395
RMSD of the common residues= 1.485 TM-score = 0.9740 (d0= 7.21) MaxSub-score= 0.9450 (d0= 3.50)
GDT-TS-score= 0.9530 %(d<1)=0.8797 %(d<2)=0.9649 %(d<4)=0.9825 %(d<8)=0.9850 %
GDT-HA-score= 0.8584 %(d<0.5)=0.6065 %(d<1)=0.8797 %(d<2)=0.9649 %(d<4)=0.9825 %
https://zhanggroup.org/TM-score/tmp/578688.html
CYP105B
>CYP105B1---- 1234567890 1234567890 1234567890 1234567890 1234567890 ----0001 MTTAERTAPP DALTVPASRA PGCPFDPAPD VTEAARTEPV TRATLWDGSS 00500051 CWLVTRHQDV RAVLGDPRFS ADAHRTGFPF LTAGGREIIG TNPTFLRMDD 01000101 PEHARLRRML TADFIVKKVE AMRPEVQRLA DDLVDRMTTG RTSADLVTEF 01500151 ALPLPSLVIC LLLGVPYEDH AFFQERSRVL LTLRSTPEEV RAAQDELLEY 02000201 LARLARTKRE RPDDAIISRL VARGELDDTQ IATMGRLLLV AGHETTANMT 02500251 ALSTLVLLRN PDQLARLRAE PALVKGAVEE LLRYLTIVHN GVPRIATEDV 03000301 LIGGRTIAAG EGVLCMISSA NRDAEVFPGG DDLDVARDAR RHVAFGFGVH 03500351 QCLGQPLARV ELQIAIETLL RRLPDLRLAV PHEEIPFRGD MAIYGVHSLP 04000401 IAWCYP105B
Heme Docked
Heme Docked
PDBj
PDBj
Alphafold result (localcolabfold using AF2 parameters)spectrum b, rainbow_rev, maximum=100, minimum=50CYP105A1_mode3magenta
TM-alignmodel3 of CYP105B1 in thick and model3 of CYP105A1 in thin wirefamesResidues with d<5A in red
TM-Score (CYP105B1 vs CYP105A1)Number of residues in common= 403
RMSD of the common residues= 6.338 TM-score = 0.7321 (d0= 7.27) MaxSub-score= 0.3880 (d0= 3.50)
GDT-TS-score= 0.5086 %(d<1)=0.2956 %(d<2)=0.3571 %(d<4)=0.5345 %(d<8)=0.8473 %
GDT-HA-score= 0.3344 %(d<0.5)=0.1502 %(d<1)=0.2956 %(d<2)=0.3571 %(d<4)=0.5345 %
https://zhanggroup.org/TM-score/tmp/619823.html
TM-Score (CYP105B1 vs CYP105A1)Number of residues in common= 403
RMSD of the common residues= 6.338 TM-score = 0.7321 (d0= 7.27) MaxSub-score= 0.3880 (d0= 3.50)
GDT-TS-score= 0.5086 %(d<1)=0.2956 %(d<2)=0.3571 %(d<4)=0.5345 %(d<8)=0.8473 %
GDT-HA-score= 0.3344 %(d<0.5)=0.1502 %(d<1)=0.2956 %(d<2)=0.3571 %(d<4)=0.5345 %
https://zhanggroup.org/TM-score/tmp/619823.html
CYP105B
>CYP105B1---- 1234567890 1234567890 1234567890 1234567890 1234567890 ----0001 MTTAERTAPP DALTVPASRA PGCPFDPAPD VTEAARTEPV TRATLWDGSS 00500051 CWLVTRHQDV RAVLGDPRFS ADAHRTGFPF LTAGGREIIG TNPTFLRMDD 01000101 PEHARLRRML TADFIVKKVE AMRPEVQRLA DDLVDRMTTG RTSADLVTEF 01500151 ALPLPSLVIC LLLGVPYEDH AFFQERSRVL LTLRSTPEEV RAAQDELLEY 02000201 LARLARTKRE RPDDAIISRL VARGELDDTQ IATMGRLLLV AGHETTANMT 02500251 ALSTLVLLRN PDQLARLRAE PALVKGAVEE LLRYLTIVHN GVPRIATEDV 03000301 LIGGRTIAAG EGVLCMISSA NRDAEVFPGG DDLDVARDAR RHVAFGFGVH 03500351 QCLGQPLARV ELQIAIETLL RRLPDLRLAV PHEEIPFRGD MAIYGVHSLP 04000401 IAWCYP105B
Heme Docked
Heme Docked
PDBj
PDBj