Job name:

3WPH chain A

654a57d2-21b7-4219-b7da-c1b28b595b37
Finished
Electron density map:

Differential EDM:
Models Number of gaps:5 Gap lengths: 36, 7, 7, 7, 4
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Non-trivial -61166

None
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Warning: All models are renumbered - the first residue in the structure has index 1.
Mix & match
None of the models is perfect? By clicking the button below you can download a .pdb file with the currently shown mix of models - for each gap at most one model can be selected. If none of them is checked, the gap will be left as is. Fourth and further gaps (sorted by size) can only come from one of the models.
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Slipknot S 5231 421-496 496-782 -- --
None
Topologies marked by an OK sign () are in accordance with the template topology.
Warning: Entanglement type is assigned automatically - for more complicated topologies there may be some disagreements with manually curated databases.
Model 1
DOPE (Discrete Optimized Protein Energy) score per residue. The lower the score, the better.
Since DOPE is calculated against the neighbours of a given amino acid, the scores
can vary between unmoved segments of different models. See here for more information.
Help
PDB
code		 Chain Entanglement
type		 Seq
identity		 Total gap
coverage		 Total gap
identity		 RMSD [Å] Pairwise alignment to the target: gap


3W3G
A
Unknot
36.44%
263.89%
56.75%
1.36

..Target: TLPAFLPC-ELKPH--GLVDCNWLFLKSVPRFSAAASCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKWNCPPTGLSPLHFSCHMTIEPRTFLAMRTLEELNLSYNGITTVPR-LPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIEC-GQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSENFLYESITHTNAFQNLTRLRKLNLSFNYRKKVSFARLHLASSFKNLVSLQELNMNGIFFRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTLSEATPEEADDAEQEELLSA-DPHP--APLSTPASKNFMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQPFSMKGIGHQFSFVTHLSMLQSLSLAHNDIHTRVSSH-LNSNSVRFLDFSGNGMGRMW-DEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWF-GPIVMQLTVLDVRSNPLHCAC----GAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRSIFAQDLRLC
Template: ---RSYPCDEKKQNDSVIAECSNRRLQEVPQ----TVGKYVTELDLSDNFITHITNESFQGLQNLTKINLNHN-PNV--------NGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLPESLTELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCE-KTNIEDGVFETLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGLINLTLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLSSTSLRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLSFNYIKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPNLSTINLGINFIKQIDFKLFQNFSNLEIIYLSENRIS-PLVK-------------------FDPHSNFYHFTRPLIK---PQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQVLSGTEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRIAGVTHHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRLDILWNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELHINDNMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLSHNRISHLPSGFLSEVSSLKHLDLSSNLLKTINKSALETKTTTKLSMLELHGNPFECTCDIGDFRRWMDEHLNV--KIPRLVD-VICASPGDQRGKSI--VSLEL-

4PUF
A
Unknot
26.54%
307.14%
87.30%
1.25

..Target: TL---------PAFLPC--ELKPHGLVDC----------NWLFLKSVPRFSAAASCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKWNCPPTGLSPLHF-SCHMTIEPRTFLAMRTLEELNLSYNGITTVP-RLPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSEN---FLYESITHTNAFQNLTRLRKLNLSFNYRKKVSFARLHLASSFKNLVSLQE----LNMNGIF-FRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTLSEATPEEADDAEQEELLSADPHPAPLSTPASKNFMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLPLTNLQVLDLSHNKLDLYHWKSFSELPQLQALDLSYNSQPFSMKGIGHQFSFVTHLSMLQSLSLAHNDI-HTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKL-----DLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFLPNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMQLTVLDVRSNPLHCACGAAFVDLLLEV-QTKVPGLANGVKCGSPGQLQGRSIFAQDLRLC
Template: ELIWSEWVKEAPAKEAANREEAVQRMRDCLKNNKTELRLKILGLTTIP----AYIPEQITTLILDNNELKSL-------PENL-QGNIK---------TLYANSNQLTSIPAT--LPDTIQEMELSINRITELPERLPSALQSLDLFHNKISCLPEN------------LPEELRYLSVYDNSIRTLP-AHLP-SEITHLNVQSNSLTALPETLPPGLKTLEAGENALTSL-PASLPP--ELQVLDV----------------------------------------------------------------SKNQITVLPETLPPTITTLDVSRNALTNLPEN----LPAALQIMQASRNNLVRLPESLPHFRGEGPQPTRIIVEYNPFSERTIQNMQRLMSSVDYQGPRVLFAMGDFSIVR--------VTRP--LHQAVQGWLTSLEEEDVNQWRAFEAEANAAAFSGFLD------YLGDTQNTRHPDFKEQVSAWLMR-----LAEDS---ALRETVFIIAMNATISCEDRVTL-AYHQMQEATL-----------------VHDAERGAFDSHLA---ELIMAGREIFRLEQIESLAREKVKRLFFI--------DEVEVFLGFQNQLRESLSLTTMTRDMRFYNVSGITESDLDEAEIRIKMAENRD----FHKWFAL-----------WGPWHKVL---------------------ERIAPE------EWREMMAKRDECIETD-EYQSRVNAELE--DLR---------AIGIKIMEEINQTLFTEIMENI-------LLKKEVSSLMSAYW

1G9U
A
Unknot
37.11%
176.98%
30.56%
1.26

..Target: TLPAFLPCELKPHGLVDCNWLFLKSVPRFSAAASCSNITRLSLISNRIHHLHNSDFVHLSNLRQLNLKW--NCPPTGLSPLHFSCHMTIEPRTFLAMRTLEELNLSYNGITTVPRLPSSLVNLSLSHTNILVLDANSLAGLYSLRVLFMDGNCYYKNPCTGAVKVTPGALLGLSQLTHLSLKYNNLTKVPRQLPPSLEYLLVSYNLIVKLGPEDLAQLTSLRVLDVGGNCRRCDHAPNPCIECGQKSLHLHPETFHHLSHLEGLVLKDSSLHTLNSSWFQGLVQLSVLDLSENFLYESITHTNAFQNLTRLRKLNLSFNYRKKVSFARLHLASSFKNLVSLQELNMNGIFFRLLNKYTLRWLADLPKLHTLHLQMNFINQAQLSIFGTFRALRFVDLSDNRISGPSTLSEATPEEADDAEQEELLSADPHPAPLSTPASKNFMDRCKNFKFTMDLSRNNLVTIKPEMFVQLSRLQCLSLSHNSIAQAVNGSQFLP-LTNLQVLDLSHNKLDLYHWKSFSEL-PQLQALDLSYNSQPFSMKGIGHQFSFVTHLSMLQSLSLAHNDIHTRVSSHLNSNSVRFLDFSGNGMGRMWDEGGLYLHFFQGLSGLLKLDLSQNNLHILRPQNLDNLPKSLKLLSLRDNYLSFFNWTSLSFL-PNLEVLDLAGNQLKALTQGTLPNGTLLQKLDVSSNSIVSVVPAFFALAVELKEVNLSHNILKTVDRSWFGPIVMQ-LTVLDVRSNPLHCACGAAFVDLLLEVQTKVPGLANGVKCGSPGQLQGRSIFAQDLRL-C
Template: -----------------------KSKTEYYNAWS---------------------------------EWERNAPP-GNGEQR---EMAVSRLRDCLDRQAHELELNNLGLSSLPELP--------PHLESLVASCNSLT-----------------------------ELPELPQSLKSLLVDNNNLKALSDLPPLLEYLGVSNNQLEKL-PE------------------------------------------------------------LQNSSF-----LKIIDVDNN-------------SLKKLPDLPPSLEF----------IAAGNNQLEELPE------------------LQNLPFLTAIY------------------------------------------------------AD-----------------------------NNSLKKLPD----------LPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLL--KTLPDLPPSLEAL----------------------------------------------------------------------------------------NVRDNYLTDLPELPQSLTFLDVSEN-----IFSGLSELPPNLYYLNASSNEIRSLCD--LP--PSLEELNVSNNKLIE-LP---ALPPRLERLIASFNHLAEV------PELPQNLKQLHVEYNP----------------LREFPDIPESV---------------EDLRMNS
Help
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

PSTLSEATPEEADDAEQEELLSA-DPHP--APLSTPASKNFMDRC
3W3G A Unknot 13.89% 38.89%

PLVK-------------------FDPHSNFYHFTRPLIK---PQC
4PUF A Unknot 19.44% 100.00%

P--LHQAVQGWLTSLEEEDVNQWRAFEAEANAAAFSGFLD--
1G9U A Unknot 5.56% 5.56%

----------------------AD------------------
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

PTGLSPLHFSCHM
3W3G A Unknot 0.00% 0.00%

NV--------NGL
4PUF A Unknot 28.57% 71.43%

-----TLYANSNQL
1G9U A Unknot 0.00% 71.43%

P-GNGEQR---EM
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

FNYRKKVSFARLH
3W3G A Unknot 14.29% 100.00%

FNYIKGSYPQHIN
4PUF A Unknot 14.29% 57.14%

EN----LPAALQI
1G9U A Unknot 0.00% 0.00%

LEF----------
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

YNSQPFSMKGIGH
3W3G A Unknot 28.57% 100.00%

YNSHYFRIAGVTH
4PUF A Unknot 0.00% 28.57%

--------VHDAE
1G9U A Unknot 0.00% 0.00%

-------------
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

PRFSAAASCS
3W3G A Unknot 0.00% 25.00%

PQ----TVGK
4PUF A Unknot 25.00% 50.00%

P----AYIPE
1G9U A Unknot 25.00% 100.00%

TEYYNAWS--

Models
Similarity profile
Modelling alignment
Raw knot fingerprint matrices:
Model_1

Wed Jul 26 06:59:44 2017	JOB CREATED : 654a57d2-21b7-4219-b7da-c1b28b595b37
Wed Jul 26 07:00:01 2017	STATUS CHANGED : N -> R
Wed Jul 26 07:00:01 2017	INFO : JOB STARTED AT: 2017-07-26 07:00:01.962656
Wed Jul 26 07:00:01 2017	INFO : METHOD: 1
Wed Jul 26 07:00:02 2017	INFO : Precalculated profile found...
Wed Jul 26 07:00:02 2017	INFO : Homologue pool found...
Wed Jul 26 07:00:02 2017	INFO : Verifying structure sequences of homologues...
Wed Jul 26 07:10:02 2017	INFO : Starting homologue filtering...
Wed Jul 26 07:10:53 2017	INFO : Getting structures from PDB...
Wed Jul 26 07:11:12 2017	INFO : Creating modelling alignment...
Wed Jul 26 07:11:12 2017	INFO : Modelling...
Wed Jul 26 08:06:07 2017	INFO : Model 1 built
Wed Jul 26 08:06:07 2017	INFO : 1/5 gaps will be remodelled
Wed Jul 26 08:45:20 2017	INFO : Validating Calpha distances...
Wed Jul 26 08:45:20 2017	INFO : Model 1 distances correct: True
Wed Jul 26 08:45:20 2017	INFO : Modelling...
Wed Jul 26 09:41:08 2017	INFO : Model 2 built
Wed Jul 26 09:41:08 2017	INFO : 1/5 gaps will be remodelled
Wed Jul 26 10:20:42 2017	INFO : Validating Calpha distances...
Wed Jul 26 10:20:42 2017	INFO : Model 2 distances correct: False
Wed Jul 26 10:20:42 2017	INFO : Modelling...
Wed Jul 26 11:14:55 2017	INFO : Model 3 built
Wed Jul 26 11:14:55 2017	INFO : 1/5 gaps will be remodelled
Wed Jul 26 11:54:52 2017	INFO : Validating Calpha distances...
Wed Jul 26 11:54:52 2017	INFO : Model 3 distances correct: False
Wed Jul 26 11:54:52 2017	INFO : Modelling...
Wed Jul 26 12:49:52 2017	INFO : Model 4 built
Wed Jul 26 12:49:52 2017	INFO : 1/5 gaps will be remodelled
Wed Jul 26 13:29:04 2017	INFO : Validating Calpha distances...
Wed Jul 26 13:29:04 2017	INFO : Model 4 distances correct: False
Wed Jul 26 13:29:04 2017	INFO : Modelling...
Wed Jul 26 14:24:52 2017	INFO : Model 5 built
Wed Jul 26 14:24:52 2017	INFO : 1/5 gaps will be remodelled
Wed Jul 26 15:04:08 2017	INFO : Validating Calpha distances...
Wed Jul 26 15:04:08 2017	INFO : Model 5 distances correct: False
Wed Jul 26 15:04:19 2017	INFO : Finished modelling
Wed Jul 26 15:04:19 2017	STATUS CHANGED : R -> P
Wed Jul 26 15:04:19 2017	INFO : Checking topology...
Thu Jul 27 06:11:56 2017	INFO : Knot matrices done...
Thu Jul 27 06:12:37 2017	INFO : Some knots found!
Thu Jul 27 06:12:38 2017	INFO : No lassos found...
Thu Jul 27 06:12:38 2017	INFO : Finishing...
Thu Jul 27 06:12:38 2017	INFO : Job done
Thu Jul 27 06:12:38 2017	STATUS CHANGED : P -> F
Thu Jul 27 06:12:38 2017	STATUS CHANGED : F -> F
GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling