Job name:

SMIESZEK(3NKQ chain A)

8af968fd-2aaa-4c46-8e60-6fb368d9228a
Finished
Warning: Knot detection did not finish.
Models Number of gaps:2 Gap lengths: 15, 10
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Err -94619
Model 2 Err -94525
Model 3 Err -94089
Model 4 Err -94172
Model 5 Non-trivial -94090
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 Lasso L +2C -- -- 106-300
Model 2 Lasso L +2C -- -- 106-300
Model 3 Lasso L +2C -- -- 106-300
Model 4 Lasso L +2C -- -- 106-300
Model 5 Lasso L +2C -- -- 106-300
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


3NKM

A

S +31

100.00%

200.00%

200.00%

0.31

..Target: WTNTSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIRVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRPKIPNNLKYDPKAIIANLTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDLHLLVERRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTLPEEVSRPNYPGIMYLQSDFDLGCTCDDKNKLEELNKRLHTKGSTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWTYFQRVLVKKYASERNGVNVISGPIFDYNYNGLRDIEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE
Template: WTNTSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIRVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRPKIPNNLKYDPKAIIANLTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDLHLLVERRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTLPEEVSRPNYPGIMYLQSDFDLGCTCDDKNKLEELNKRLHTKGSTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWTYFQRVLVKKYASERNGVNVISGPIFDYNYNGLRDIEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE

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

CDDKNKLEELNKRLHTKGSTE

3NKM A S +31 100.00% 100.00%

CDDKNKLEELNKRLHTKGSTE

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

KPLDVYKKPSGKCFFQ

3NKM A S +31 100.00% 100.00%

KPLDVYKKPSGKCFFQ


Sat Sep  2 17:03:42 2017	JOB CREATED : 8af968fd-2aaa-4c46-8e60-6fb368d9228a
Sat Sep  2 17:04:02 2017	STATUS CHANGED : N -> R
Sat Sep  2 17:04:02 2017	INFO : JOB STARTED AT: 2017-09-02 17:04:02.439044
Sat Sep  2 17:04:02 2017	INFO : METHOD: 1
Sat Sep  2 17:04:02 2017	INFO : Precalculated profile found...
Sat Sep  2 17:04:02 2017	INFO : Homologue pool found...
Sat Sep  2 17:04:02 2017	INFO : Verifying structure sequences of homologues...
Sat Sep  2 17:05:03 2017	INFO : Starting homologue filtering...
Sat Sep  2 17:06:10 2017	INFO : Getting structures from PDB...
Sat Sep  2 17:06:18 2017	INFO : Creating modelling alignment...
Sat Sep  2 17:06:18 2017	INFO : Modelling...
Sat Sep  2 17:38:48 2017	INFO : Model 1 built
Sat Sep  2 17:38:48 2017	INFO : Validating Calpha distances...
Sat Sep  2 17:38:48 2017	INFO : Model 1 distances correct: True
Sat Sep  2 17:38:48 2017	INFO : Modelling...
Sat Sep  2 18:36:42 2017	INFO : Model 2 built
Sat Sep  2 18:36:42 2017	INFO : Validating Calpha distances...
Sat Sep  2 18:36:42 2017	INFO : Model 2 distances correct: True
Sat Sep  2 18:36:42 2017	INFO : Modelling...
Sat Sep  2 19:08:00 2017	INFO : Model 3 built
Sat Sep  2 19:08:00 2017	INFO : Validating Calpha distances...
Sat Sep  2 19:08:00 2017	INFO : Model 3 distances correct: True
Sat Sep  2 19:08:00 2017	INFO : Modelling...
Sat Sep  2 19:50:10 2017	INFO : Model 4 built
Sat Sep  2 19:50:10 2017	INFO : Validating Calpha distances...
Sat Sep  2 19:50:10 2017	INFO : Model 4 distances correct: True
Sat Sep  2 19:50:10 2017	INFO : Modelling...
Sat Sep  2 20:36:08 2017	INFO : Model 5 built
Sat Sep  2 20:36:08 2017	INFO : Validating Calpha distances...
Sat Sep  2 20:36:08 2017	INFO : Model 5 distances correct: True
Sat Sep  2 20:37:22 2017	INFO : Finished modelling
Sat Sep  2 20:37:22 2017	STATUS CHANGED : R -> P
Sat Sep  2 20:37:22 2017	INFO : Checking topology...
Sat Sep  2 20:37:23 2017	INFO : Knot matrices done...
Sat Sep  2 20:37:23 2017	INFO : No knots found...
Sat Sep  2 20:38:14 2017	INFO : Some lassos found!
Sat Sep  2 20:38:14 2017	INFO : Finishing...
Sat Sep  2 20:38:15 2017	INFO : Job done
Sat Sep  2 20:38:15 2017	STATUS CHANGED : P -> F
Sat Sep  2 20:38:15 2017	STATUS CHANGED : F -> F

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