CYPSD - CYP105

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).

D. R. Nelson's

Bacteria_1

Bacteria_2

Bacteria_3

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"

runner_P450.py

align_P450.py

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 ELPVTW

Alphafold2

105A1_m3.pdb

CYP105A1.fasta

Heme Docked

PDBj 1.5Å

2zbx

CYP105A1 WT
(H308Q from Nelson's)

Alphafold2

105A1_m3.pdb

105A1_m4.pdb

105A1_m3.pdb

105A1_m2.pdb

105A1_m5.pdb

Alphafold2_ptm

105A1_m3p.pdb

105A1_m2p.pdb

105A1_m4p.pdb

105A1_m5p.pdb

105A1_m1p.pdb

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

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 IAW

Alphafold2

105B1_m3.pdb

CYP105B1.fasta

Heme Docked

PDBj

Alphafold2

105B1_m3.pdb

105B1_m2.pdb

105B1_m1.pdb

105B1_m5.pdb

105B1_m4.pdb

Alphafold2_ptm

105B1_m5p.pdb

105B1_m3p.pdb

105B1_m2p.pdb

105B1_m4p.pdb

105B1_m1p.pdb

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

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 IAW