Job name:

ZARAZ GO ZAWIESZE(5WRG chain A)

c4faf7e8-dd57-43b2-993d-1dbd6c222944
Finished
Models Number of gaps:4 Gap lengths: 26, 17, 15, 8
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Non-trivial -60985

Model 2 Non-trivial -50087

Model 3 Non-trivial -50529

None
Reload
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.
Warning: JSmol may at times display gaps where there are none - due to some overlaps in models. This does not indicate presence of gaps in downloaded structure!
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Slipknot S 5231 419-776 776-786 -- --
Lasso L -1C -- -- 106-159
Model 2 Slipknot S 5231 444-772 772-785 -- --
Lasso L -1C -- -- 106-159
Model 3 Slipknot S 5251+31 423-776 776-786 -- --
Lasso L -1C -- -- 106-159
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
Model 2
Model 3
Model 1
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.
PDB
code
Chain Entanglement
type
Seq
identity
Total gap
coverage
Total gap
identity
RMSD [Å] Pairwise alignment to the target: gap


2DD8

S

Unknot

98.96%

62.50%

62.50%

1.15

..Target: TFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLLASTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFT
Template: ------------------------------------------------------------NLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATV------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CG

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

VTLADAGFMKQYGECLGDINARDLICAQKFNG

2DD8 S Unknot 0.00% 0.00%

--------------------------------

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

VSGTATAGWTFGAGAALQIPFAM

2DD8 S Unknot 0.00% 0.00%

-----------------------

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

ASYHTVSLLASTSQKSIVAYT

2DD8 S Unknot 0.00% 0.00%

---------------------

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

LLNAPATVCGPKLS

2DD8 S Unknot 62.50% 62.50%

LLNAPATV------


Models
Similarity profile
Modelling alignment
Raw knot fingerprint matrices:
Model_1
Model_2
Model_3

Sat Aug  5 17:45:43 2017	JOB CREATED : c4faf7e8-dd57-43b2-993d-1dbd6c222944
Sat Aug  5 17:46:01 2017	STATUS CHANGED : N -> R
Sat Aug  5 17:46:01 2017	INFO : JOB STARTED AT: 2017-08-05 17:46:01.812223
Sat Aug  5 17:46:01 2017	INFO : METHOD: 2
Sat Aug  5 17:46:01 2017	INFO : Building Profile...
Sat Aug  5 17:46:01 2017	INFO : --E-value set to 0.001--
Sat Aug  5 18:07:54 2017	INFO : Homologue pool found...
Sat Aug  5 18:07:54 2017	INFO : Verifying structure sequences of homologues...
Sat Aug  5 18:09:49 2017	INFO : Starting homologue filtering...
Sat Aug  5 18:10:34 2017	INFO : Getting structures from PDB...
Sat Aug  5 18:10:36 2017	INFO : Creating modelling alignment...
Sat Aug  5 18:10:36 2017	INFO : Modelling...
Sat Aug  5 19:06:52 2017	INFO : Model 1 built
Sat Aug  5 19:06:52 2017	INFO : Validating Calpha distances...
Sat Aug  5 19:06:52 2017	INFO : Model 1 distances correct: True
Sat Aug  5 19:06:52 2017	INFO : Modelling...
Sat Aug  5 20:50:36 2017	INFO : Model 2 built
Sat Aug  5 20:50:36 2017	INFO : Validating Calpha distances...
Sat Aug  5 20:50:36 2017	INFO : Model 2 distances correct: True
Sat Aug  5 20:50:36 2017	INFO : Modelling...
Sat Aug  5 22:38:11 2017	INFO : Model 3 built
Sat Aug  5 22:38:11 2017	INFO : 1/4 gaps will be remodelled
Sat Aug  5 23:20:01 2017	INFO : Validating Calpha distances...
Sat Aug  5 23:20:01 2017	INFO : Model 3 distances correct: True
Sat Aug  5 23:20:01 2017	INFO : Modelling...
Sun Aug  6 01:12:58 2017	INFO : Model 4 built
Sun Aug  6 01:12:58 2017	INFO : 1/4 gaps will be remodelled
Sun Aug  6 01:49:22 2017	INFO : Validating Calpha distances...
Sun Aug  6 01:49:22 2017	INFO : Model 4 distances correct: False
Sun Aug  6 01:49:22 2017	INFO : Modelling...
Sun Aug  6 03:27:47 2017	INFO : Model 5 built
Sun Aug  6 03:27:47 2017	INFO : 1/4 gaps will be remodelled
Sun Aug  6 04:07:54 2017	INFO : Validating Calpha distances...
Sun Aug  6 04:07:54 2017	INFO : Model 5 distances correct: False
Sun Aug  6 04:08:24 2017	INFO : Finished modelling
Sun Aug  6 04:08:24 2017	STATUS CHANGED : R -> P
Sun Aug  6 04:08:24 2017	INFO : Checking topology...
Sun Aug  6 12:36:31 2017	INFO : Knot matrices done...
Sun Aug  6 12:41:29 2017	INFO : Some knots found!
Sun Aug  6 12:41:30 2017	INFO : Some lassos found!
Sun Aug  6 12:41:30 2017	INFO : Finishing...
Sun Aug  6 12:41:31 2017	INFO : Job done
Sun Aug  6 12:41:31 2017	STATUS CHANGED : P -> F
Sun Aug  6 12:41:31 2017	STATUS CHANGED : F -> F

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