Job name:

3WPI chain A

e5349089-3709-4024-9fe5-7c75ef77de2c
Finished
Electron density map:

Differential EDM:
Models Number of gaps:5 Gap lengths: 36, 7, 6, 5, 5
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Unknot -68741

Model 2 Non-trivial -66387

Model 3 Non-trivial -67547

Model 4 Unknot -68069

Model 5 Unknot -67462

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 2 Lasso L -1N -- -- 444-474 -413
Model 3 Lasso L -1N -- -- 444-474 -414
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 2
Model 3
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%
278.89%
61.51%
1.35

..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%
364.76%
93.73%
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%
165.56%
45.56%
1.20

..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

NYRKKVSFARLHL
3W3G A Unknot 14.29% 100.00%

NYIKGSYPQHINI
4PUF A Unknot 14.29% 71.43%

N----LPAALQIM
1G9U A Unknot 0.00% 0.00%

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

NSQPFSMKGIGH
3W3G A Unknot 33.33% 100.00%

NSHYFRIAGVTH
4PUF A Unknot 0.00% 33.33%

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

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

PRFSAAASCSN
3W3G A Unknot 0.00% 40.00%

PQ----TVGKY
4PUF A Unknot 20.00% 60.00%

P----AYIPEQ
1G9U A Unknot 40.00% 100.00%

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

GLSPLHFSCHM
3W3G A Unknot 0.00% 0.00%

--------NGL
4PUF A Unknot 40.00% 100.00%

---TLYANSNQL
1G9U A Unknot 0.00% 60.00%

GNGEQR---EM

Models
Similarity profile
Modelling alignment

Sun Jul 23 14:59:45 2017	JOB CREATED : e5349089-3709-4024-9fe5-7c75ef77de2c
Mon Jul 24 01:45:01 2017	STATUS CHANGED : N -> R
Mon Jul 24 01:45:01 2017	INFO : JOB STARTED AT: 2017-07-24 01:45:01.726728
Mon Jul 24 01:45:01 2017	INFO : METHOD: 1
Mon Jul 24 01:45:01 2017	INFO : Precalculated profile found...
Mon Jul 24 01:45:01 2017	INFO : Homologue pool found...
Mon Jul 24 01:45:01 2017	INFO : Verifying structure sequences of homologues...
Mon Jul 24 02:00:55 2017	INFO : Starting homologue filtering...
Mon Jul 24 02:02:05 2017	INFO : Getting structures from PDB...
Mon Jul 24 02:02:30 2017	INFO : Creating modelling alignment...
Mon Jul 24 02:02:30 2017	INFO : Modelling...
Mon Jul 24 03:16:50 2017	INFO : Model 1 built
Mon Jul 24 03:16:50 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 03:46:12 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:46:12 2017	INFO : Model 1 distances correct: True
Mon Jul 24 03:46:12 2017	INFO : Modelling...
Mon Jul 24 05:16:01 2017	INFO : Model 2 built
Mon Jul 24 05:16:01 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 05:44:17 2017	INFO : Validating Calpha distances...
Mon Jul 24 05:44:17 2017	INFO : Model 2 distances correct: True
Mon Jul 24 05:44:17 2017	INFO : Modelling...
Mon Jul 24 07:03:44 2017	INFO : Model 3 built
Mon Jul 24 07:03:44 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 07:27:56 2017	INFO : Validating Calpha distances...
Mon Jul 24 07:27:56 2017	INFO : Model 3 distances correct: True
Mon Jul 24 07:27:56 2017	INFO : Modelling...
Mon Jul 24 08:38:05 2017	INFO : Model 4 built
Mon Jul 24 08:38:05 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 09:00:35 2017	INFO : Validating Calpha distances...
Mon Jul 24 09:00:35 2017	INFO : Model 4 distances correct: True
Mon Jul 24 09:00:35 2017	INFO : Modelling...
Mon Jul 24 09:58:02 2017	INFO : Model 5 built
Mon Jul 24 09:58:02 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 10:16:43 2017	INFO : Validating Calpha distances...
Mon Jul 24 10:16:43 2017	INFO : Model 5 distances correct: True
Mon Jul 24 10:17:40 2017	INFO : Finished modelling
Mon Jul 24 10:17:40 2017	STATUS CHANGED : R -> P
Mon Jul 24 10:17:40 2017	INFO : Checking topology...
Mon Jul 24 11:12:11 2017	INFO : Knot matrices done...
Mon Jul 24 11:13:27 2017	INFO : No knots found...
Mon Jul 24 11:13:28 2017	INFO : Some lassos found!
Mon Jul 24 11:13:28 2017	INFO : Finishing...
Mon Jul 24 11:13:29 2017	INFO : Job done
Mon Jul 24 11:13:29 2017	STATUS CHANGED : P -> F
Mon Jul 24 11:13:29 2017	STATUS CHANGED : F -> F
GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling