Job name:

5TJ6A_dbase(5TJ6 chain A)

c9a0d3d1-598c-4d74-9403-aec9c612be1d
Finished
Models Number of gaps:6 Gap lengths: 85, 35, 26, 10, 6, 6
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Non-trivial -120746

Model 2 Non-trivial -120524

Model 3 Non-trivial -119800

Model 4 Non-trivial -120452

Model 5 Non-trivial -103862

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 Knot S 52-31 468-970 -- -- --
Lasso L -1C -- -- 474-806
Model 2 Slipknot S 52-31 473-970 970-1051 -- --
Lasso L -1C -- -- 474-806
Model 3 Slipknot S 52-31 134-1049 1049-1050 -- --
Lasso L -1C -- -- 474-806
Model 4 Knot S 52-31 467-970 -- -- --
Lasso L -1C -- -- 474-806
Model 5 Slipknot S 52-31 466-970 970-1051 -- --
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
Model 1
Model 2
Model 3
Model 4
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


3NAF

A

Unknot

64.66%

216.59%

70.20%

1.16

..Target: RQWYSFLASSLVTFGSGLVVIIIYRIVLWLCCRKKKCIQVSNPVPTARTTSLDQKSFMKNSDPEIGWMTEAKDWAGELISGQTTTGRILVGLVFLLSIASLIIYFIDASTNTSVETCLPWSSSTTQQVDLAFNVFFMIYFFIRFVAANDKLWFWVELFSFVDYFTIPPSFVAIYLDRNWLGLRFLRALRLMSIPDILTYLNVLKTSTLIRLVQLVVSFVSLWLTAAGFLHLLENSGDPFFDFGNAQHLTYWECLYFLMVTMSTVGFGDIFATTVLGRTFVVIFIMIFIGLFASFIPEIAEILGKRQKYGGSYKKERGKRHVVVCGYITFDSVSNFLKDFLHKDREDVDVEIVFLHKGLPGLELEGLLKRHFTQVEYFWGSVMDANDLERVKIQEADACLVLANKYCQDPDQEDAANIMRVISIKNYHSDIKVIVQLLQYHNKAYLLNIPSWDWKRGDDAVCVAELKLGFIAQSCLAPGFSTLMANLFTMRSYKPTPEMSQWQTDYMRGTGMEMYTEYLSSAFNALTFPEAAELCFSKLKLLLLAIEVRQEDTRESTLAINPGPKVKIENATQGFFIAESAEEVKRAFYYCKNCHANVSDVRQIKKCKCRPLAMFKKGAAAVLALQRTPGLAVEPDGEANDKDKSRGTSTSKAVTSFPEKRKPQSRRKPSTTLKSKSPSEDSVPPPPPPVDEPRKFDSTGMFHWCPDRPLNDCLQDRSQASASGLRNHVVVCLFADAASPLIGLRNLVMPLRASNFHYHELKPTIIVGNLDYLHREWKTLQNFPKLSILPGSPLNRANLRAVNINLCDMCVIVSAKDRNMEDPNLVDKEAILCSLNIKAMTFDDTMGLIQSSNFVPGGFSPLHENKRSQAGANVPLITELANDSNVQFLDQDDDDDPDTELYMTQPFACGTAFAVSVLDSLMSTSYFNDNALTLIRTLITGGATPELEQILAEGAGMRGGYCSPAVLANRDRCRVAQISLFDGPLAQFGQGGHYGELFVYALRHFGILCIGLYRFRDTNESVRSPSSKRYVITNPPEDFPLLPTDQVY----VLTYK
Template: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KYGGSYSAVSGRKHIVVCGHITLESVSNFLKDFLHKDRDDVNVEIVFLHNISPNLELEALFKRHFTQVEFYQGSVLNPHDLARVKIESADACLILANKYCADPDAEDASNIMRVISIKNYHPKIRIITQMLQYHNKAHLLNIPSWNWKEGDDAICLAELKLGFIAQSCLAQGLSTMLANLFSMRSFIKIEE-DTWQKYYLEGVSNEMYTEYLSSAFVGLSFPTVCELCFVKLKLLMIAIEYKSAN-RESRILINPGNHLKIQEGTLGFFIASDAKEVKRAFFYCKACH--------------------------------------------------XXXXXXXXXXXXXXXXSPKLMR------------HD------------KKYDSTGMFHWCAPKEIEKVILTRSEAAMTVLSGHVVVCIFGDVSSALIGLRNLVMPLRASNFHYHELKHIVFVGSIEYLKREWETLHNFPKVSILPGTPLSRADLRAVNINLCDMCVILSANQNNIDDTSLQDKECILASLNIKSMQFD--------------------------TGVNIPIITELVNDTNVQFLDQDDDDDPDTELYLTQPFACGTAFAVSVLDSLMSATYFNDNILTLIRTLVTGGATPELEALIAEENALRGGYSTPQTLANRDRCRVAQLALLDGPFADLGDGGCYGDLFCKALKTYNMLCFGIYRLRDAHLSTPSQCTKRYVITNPPYEFELVPTDLIFCLMQFDHNA


2Q67

A

Unknot

35.58%

50.00%

20.00%

1.05

..Target: RQWYSFLASSLVTFGSGLVVIIIYRIVLWLCCRKKKCIQVSNPVPTARTTSLDQKSFMKNSDPEIGWMTEAKDWAGELISGQTTTGRILVGLVFLLSIASLIIYFIDASTNTSVETCLPWSSSTTQQVDLAFNVFFMIYFFIRFVAANDKLWFWVELFSFVDYFTIPPSFVAIYLDRNWLGLRFLRALRLMSIPDILTYLNVLKTSTLIRLVQLVVSFVSLWLTAAGFLHLLENSGDPFFDFGNAQHLTYWECLYFLMVTMSTVGFGDIFATTVLGRTFVVIFIMIFIGLFASFIPEIAEILGKRQKYGGSYKKERGKRHVVVCGYITFDSVSNFLKDFLHKDREDVDVEIVFLHKGLPGLELEGLLKRHFTQVEYFWGSVMDANDLERVKIQEADACLVLANKYCQDPDQEDAANIMRVISIKNYHSDIKVIVQLLQYHNKAYLLNIPSWDWKRGDDAVCVAELKLGFIAQSCLAPGFSTLMANLFTMRSYKPTPEMSQWQTDYMRGTGMEMYTEYLSSAFNALTFPEAAELCFSKLKLLLLAIEVRQEDTRESTLAINPGPKVKIENATQGFFIAESAEEVKRAFYYCKNCHANVSDVRQIKKCKCRPLAMFKKGAAAVLALQRTPGLAVEPDGEANDKDKSRGTSTSKAVTSFPEKRKPQSRRKPSTTLKSKSPSEDSVPPPPPPVDEPRKFDSTGMFHWCPDRPLNDCLQDRSQASASGLRNHVVVCLFADAASPLIGLRNLVMPLRASNFHYHELKPTIIVGNLDYLHREWKTLQNFPKLSILPGSPLNRANLRAVNINLCDMCVIVSAKDRNMEDPNLVDKEAILCSLNIKAMTFDDTMGLIQSSNFVPGGFSPLHENKRSQAGANVPLITELANDSNVQFLDQDDDDDPDTELYMTQPFACGTAFAVSVLDSLMSTSYFNDNALTLIRTLITGGATPELEQILAEGAGMRGGYCSPAVLANRDRCRVAQISLFDGPLAQFGQGGHYGELFVYALRHFGILCIGLYRFRDTNESVRSPSSKRYVITNPPEDFPLLPTDQVYVLTYK
Template: ------------------------------------------------------------------------------------------MLSFLLTLKRM------------LRACL------RAWKDKEFQVLF----------------------------------------------------------------------------------------VLTILTLI--SGTIFYS--TVEGLRPIDALYFSVVTLTTVGAGNFSPQTDFGKIFTILY--IFIG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IGL-------------------------VFGFI--HKLAVNVQL

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

CKCRPLAMFKKGAAAVLALQRTPGLAVEPDGEANDKDKSRGTSTSKAVTSFPEKRKPQSRRKPSTTLKSKSPSEDSVPPPPPPVDEPRKFD

3NAF A Unknot 3.53% 29.41%

---------------------------------------XXXXXXXXXXXXXXXXSPKLMR------------HD------------KKYD

2Q67 A Unknot 0.00% 0.00%

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

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

WLCCRKKKCIQVSNPVPTARTTSLDQKSFMKNSDPEIGWMT

3NAF A Unknot 0.00% 0.00%

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

2Q67 A Unknot 0.00% 0.00%

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

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

FDDTMGLIQSSNFVPGGFSPLHENKRSQAGAN

3NAF A Unknot 0.00% 3.85%

FD--------------------------TGVN

2Q67 A Unknot 0.00% 0.00%

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

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

STNTSVETCLPWSSST

3NAF A Unknot 0.00% 0.00%

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

2Q67 A Unknot 20.00% 50.00%

-----LRACL------

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

EVRQEDTRESTL

3NAF A Unknot 33.33% 83.33%

EYKSAN-RESRI

2Q67 A Unknot 0.00% 0.00%

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

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

DTNESVRSPSSK

3NAF A Unknot 33.33% 100.00%

DAHLSTPSQCTK

2Q67 A Unknot 0.00% 0.00%

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


Sun Jul 23 14:59:07 2017	JOB CREATED : c9a0d3d1-598c-4d74-9403-aec9c612be1d
Sun Jul 23 22:30:02 2017	STATUS CHANGED : N -> R
Sun Jul 23 22:30:02 2017	INFO : JOB STARTED AT: 2017-07-23 22:30:02.701212
Sun Jul 23 22:30:02 2017	INFO : METHOD: 1
Sun Jul 23 22:30:02 2017	INFO : Precalculated profile found...
Sun Jul 23 22:30:02 2017	INFO : Homologue pool found...
Sun Jul 23 22:30:02 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 22:47:54 2017	INFO : Starting homologue filtering...
Sun Jul 23 22:49:03 2017	INFO : Getting structures from PDB...
Sun Jul 23 22:49:18 2017	INFO : Creating modelling alignment...
Sun Jul 23 22:49:18 2017	INFO : Modelling...
Mon Jul 24 01:16:55 2017	INFO : Model 1 built
Mon Jul 24 01:16:55 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 01:34:45 2017	INFO : Validating Calpha distances...
Mon Jul 24 01:34:45 2017	INFO : Model 1 distances correct: True
Mon Jul 24 01:34:45 2017	INFO : Modelling...
Mon Jul 24 02:27:52 2017	INFO : Model 2 built
Mon Jul 24 02:27:52 2017	INFO : Validating Calpha distances...
Mon Jul 24 02:27:52 2017	INFO : Model 2 distances correct: True
Mon Jul 24 02:27:52 2017	INFO : Modelling...
Mon Jul 24 04:14:39 2017	INFO : Model 3 built
Mon Jul 24 04:14:39 2017	INFO : Validating Calpha distances...
Mon Jul 24 04:14:39 2017	INFO : Model 3 distances correct: True
Mon Jul 24 04:14:39 2017	INFO : Modelling...
Mon Jul 24 07:16:03 2017	INFO : Model 4 built
Mon Jul 24 07:16:03 2017	INFO : Validating Calpha distances...
Mon Jul 24 07:16:03 2017	INFO : Model 4 distances correct: True
Mon Jul 24 07:16:03 2017	INFO : Modelling...
Mon Jul 24 09:24:47 2017	INFO : Model 5 built
Mon Jul 24 09:24:47 2017	INFO : Validating Calpha distances...
Mon Jul 24 09:24:47 2017	INFO : Model 5 distances correct: True
Mon Jul 24 09:25:55 2017	INFO : Finished modelling
Mon Jul 24 09:25:55 2017	STATUS CHANGED : R -> P
Mon Jul 24 09:25:55 2017	INFO : Checking topology...
Mon Jul 24 13:42:30 2017	INFO : Knot matrices done...
Mon Jul 24 13:54:30 2017	INFO : Some knots found!
Mon Jul 24 13:55:13 2017	INFO : Some lassos found!
Mon Jul 24 13:55:13 2017	INFO : Finishing...
Mon Jul 24 13:55:14 2017	INFO : Job done
Mon Jul 24 13:55:14 2017	STATUS CHANGED : P -> F
Mon Jul 24 13:55:14 2017	STATUS CHANGED : F -> F

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