d1opma1

DomainSCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP familyProtein
1opm_A1d1opma1A45-A200All beta proteinsNucleoplasmin-like/VP (viral coat and capsid proteins)PHM/PNGase FPeptidylglycine alpha-hydroxylating monooxygenase, PHMPeptidylglycine alpha-hydroxylating monooxygenase, PHM
1opm_A2d1opma2A201-A354All beta proteinsNucleoplasmin-like/VP (viral coat and capsid proteins)PHM/PNGase FPeptidylglycine alpha-hydroxylating monooxygenase, PHMPeptidylglycine alpha-hydroxylating monooxygenase, PHM

Alignment-based scores

AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual990.050512.3690570.95960-3.75735
dali1110.036042.6722467.34234-4.44491
tm1150.052172.8482266.52174-4.53759
fast1110.036043.1429765.54054-3.98674

In the alignments below, two upper-case letters are aligned, and two lower-case letters are NOT aligned. The superposition files are re-constructed from the corresponding alignments by minimizing the overall RMSD. In a PDB-format superposition file, the first domain is represented by chain S and the second domain is represented by chain A. The coordinates of the first domain are transformed, while the coordinates of the second domain are the same as in the original PDB file.


MANUAL alignment      superposition in PDB format     colored superposition in PyMol

1opm_A1   neclgtigpvtpldaSDFALDIRMPGVTPK--ESDTYFCMSMRLPvdEEAFVIDFKPRASmDTVHHMLLFGCNMpsstgsywfcdegtctDKANILYAWARNAPPTRlpkgvGFRVGgetgsKYFVLQVHYGDisafrdnh------KDCSGVSVHLTRvpqpl--------------------------
1opm_A2   ---------------IAGMYLMMSVDTVIPpgEKVVNADISCQYKm-YPMHVFAYRVHTH-HLGKVVSGYRVRN----------------GQWTLIGRQNPQLPQAFypvehPVDVTfg---DILAARCVFTGegrteathiggtssDEMCNLYIMYYMeakyalsfmtctknvapdmfrtipaeanipi

DALI alignment      superposition in PDB format     colored superposition in PyMol

1opm_A1   neclgtigpvtpldaSDFALDIRMPGVTPK--ESDTYFCMSMRLPVdEEAFVIDFKPRASMdTVHHMLLFGCNMpsstgsywfcdegtctDKANILYAWA-RNAPPTRLpkgVGFRVGGetgsKYFVLQVHYGdISAFRDNHKD-------CSGVSVHLTRV--------------------------pqpl
1opm_A2   ---------------IAGMYLMMSVDTVIPpgEKVVNADISCQYKM-YPMHVFAYRVHTHH-LGKVVSGYRVRN----------------GQWTLIGRQNpQLPQAFYP-veHPVDVTF---gDILAARCVFT-GEGRTEATHIggtssdeMCNLYIMYYMEakyalsfmtctknvapdmfrtipaeanipi

TM alignment      superposition in PDB format     colored superposition in PyMol

1opm_A1   NECLGTIGPVTPLDASDFALDIRMPGVTPK--ESDTYFCMSMRLPVDEEAFVIDFKPRASMDTVHHMLLFGCNMPSSTGSYWFCDEGTCTDKANILYAWARNAP-PTRLP-KGVGFRVGGETGSKYFVLQVHYGDISAFRDNHK------DCSGVSVHLTRVP-----------------------------QPL
1opm_A2   ---------------IAGMYLMMSVDTVIPPGEKVVNADISCQYKM-YPMHVFAYRVHTH-HLGKVVSGYRVRN----------------GQWTLIGRQNPQLPQAFYPVE--HPVDVTF---GDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKYALSFMTCTKNVAPDMFRTIPAEANIPI---

FAST alignment      superposition in PDB format     colored superposition in PyMol

1opm_A1   NECLGTIGPVTPLDASDFALDIRMPGVTPKE--SDTYFCMSMRLPVDEEAFVIDFKPRASMDTVHHMLLFGCNMPSSTGSYWFCDEGTCTD-KANILYAWARNAPPT--RLPKGVGFRVGGETGSKYFVLQVHYGDISAFRDNH-------KDCSGVSVHLTRVPQPL-------------------------------
1opm_A2   ---------------IAGMYLMMSVDTVIPPGEKVVNADISCQYKM-YPMHVFAYRVHTH-HLGKVVSGYRVRN-----------------GQWTLIGRQNPQLPQAFYPVEH--PVDV-TFGD--ILAARCVFT-GEGRTEATHIGGTSSDEMCNLYIMYYM-----EAKYALSFMTCTKNVAPDMFRTIPAEANIPI