Job name:

1E2L chain A

518206f3-7b74-40fc-a70e-0d3ed3846455
Finished
Electron density map:

Differential EDM:
Models Number of gaps:3 Gap lengths: 16, 8, 4
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap3rd gap
Model 1 Non-trivial -40986
Model 2 Non-trivial -41092
Model 3 Non-trivial -40866
Model 4 Non-trivial -40928
Model 5 Non-trivial -40745
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.
Pro Tip: Since you provided a structure that contains some crystallographic information you can verify our models using the wwPDB service.
Validity report for the RCSB PDB structure you were repairing can be accessed here
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Slipknot S 31 6-119 119-304 -- --
Model 2 Slipknot S 31 4-114 114-304 -- --
Model 3 Slipknot S 31 6-118 118-304 -- --
Model 4 Slipknot S 31 14-308 308-328 -- --
Model 5 Slipknot S 31 14-308 308-328 -- --
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 4
Model 5
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


1KI2

B

S +31

99.36%

187.50%

187.50%

0.72

..Target: MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIFTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE-
Template: MPTLLRVYIDGPHGMGKTTTTQLLVALG---DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLS-------------NAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEA


1E2K

B

S +31

99.68%

237.50%

237.50%

0.62

..Target: MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIFTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
Template: MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA---HAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKR----ERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAV------PQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE

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

LSGTAVPPQGAEPQSNAGPRPH

1KI2 B S +31 25.00% 25.00%

LS-------------NAGPRPH

1E2K B S +31 62.50% 62.50%

LSGTAV------PQSNAGPRPH

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

QLLVALGSRDDIVY

1KI2 B S +31 62.50% 62.50%

QLLVALG---DIVY

1E2K B S +31 100.00% 100.00%

QLLVALGSRDDIVY

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

AGSSHAPPPA

1KI2 B S +31 100.00% 100.00%

AGSSHAPPPA

1E2K B S +31 75.00% 75.00%

A---HAPPPA


Fri Dec  1 09:43:28 2017	JOB CREATED : 518206f3-7b74-40fc-a70e-0d3ed3846455
Fri Dec  1 19:51:02 2017	STATUS CHANGED : N -> R
Fri Dec  1 19:51:02 2017	INFO : JOB STARTED AT: 2017-12-01 19:51:02.763580
Fri Dec  1 19:51:02 2017	INFO : METHOD: 1
Fri Dec  1 19:51:02 2017	INFO : Precalculated profile found...
Fri Dec  1 19:51:02 2017	INFO : Homologue pool found...
Fri Dec  1 19:51:02 2017	INFO : Verifying structure sequences of homologues...
Fri Dec  1 19:53:22 2017	INFO : Starting homologue filtering...
Fri Dec  1 19:54:12 2017	INFO : Getting structures from PDB...
Fri Dec  1 19:54:21 2017	INFO : Creating modelling alignment...
Fri Dec  1 19:54:21 2017	INFO : Modelling...
Fri Dec  1 20:01:55 2017	INFO : Model 1 built
Fri Dec  1 20:01:55 2017	INFO : Validating Calpha distances...
Fri Dec  1 20:01:55 2017	INFO : Model 1 distances correct: True
Fri Dec  1 20:01:55 2017	INFO : Modelling...
Fri Dec  1 20:08:55 2017	INFO : Model 2 built
Fri Dec  1 20:08:55 2017	INFO : Validating Calpha distances...
Fri Dec  1 20:08:55 2017	INFO : Model 2 distances correct: True
Fri Dec  1 20:08:55 2017	INFO : Modelling...
Fri Dec  1 20:16:19 2017	INFO : Model 3 built
Fri Dec  1 20:16:19 2017	INFO : Validating Calpha distances...
Fri Dec  1 20:16:19 2017	INFO : Model 3 distances correct: True
Fri Dec  1 20:16:19 2017	INFO : Modelling...
Fri Dec  1 20:28:28 2017	INFO : Model 4 built
Fri Dec  1 20:28:28 2017	INFO : Validating Calpha distances...
Fri Dec  1 20:28:28 2017	INFO : Model 4 distances correct: True
Fri Dec  1 20:28:28 2017	INFO : Modelling...
Fri Dec  1 20:39:56 2017	INFO : Model 5 built
Fri Dec  1 20:39:56 2017	INFO : Validating Calpha distances...
Fri Dec  1 20:39:56 2017	INFO : Model 5 distances correct: True
Fri Dec  1 20:40:37 2017	INFO : Finished modelling
Fri Dec  1 20:40:37 2017	STATUS CHANGED : R -> P
Fri Dec  1 20:40:37 2017	INFO : Checking topology...
Fri Dec  1 20:42:38 2017	INFO : Knot matrices done...
Fri Dec  1 20:43:59 2017	INFO : Some knots found!
Fri Dec  1 20:43:59 2017	INFO : No lassos found...
Fri Dec  1 20:43:59 2017	INFO : Finishing...
Fri Dec  1 20:43:59 2017	STATUS CHANGED : P -> E
Fri Dec  1 20:43:59 2017	ERROR : Error while finishing
Fri Dec  1 20:43:59 2017	STATUS CHANGED : E -> F

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