Job name:

4WVM chain B

85e1207e-7bef-4030-8a72-1e2cc49f0f53
Finished
Electron density map:

Differential EDM:
Models Number of gaps:9 Gap lengths: 21, 17, 15, 11, 6, 5, 5, 4, 4
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Unknot -55347

Model 2 Non-trivial -54254

Model 3 Non-trivial -54068

Model 4 Unknot -52096

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.
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 2 Slipknot S 31 121-236 236-696 -- --
Model 3 Slipknot S +31 119-236 236-696 -- --
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


4B3N
A
Unknot
21.18%
727.92%
219.65%
1.09

..Target: DILVVAALGRPFTLGMLYDARNDKLIPGFTLWEDEVIEESTLESSQPSSAFEIIASDSTDDKSSLMDIEASLKASFLGGLVEVGGSAKYLNNQKKFKNQSRVTLQYKATTSFKQLMTNLGTKHVE-YSELFENIQATHVVIGILYGANAFFVFDS--NKVDSTNVQEIQGQMEAVIKKIP----SVEISGKASVQLTGEETDITNSFSCEFHGDFFLTTNPTTFEDAVKTYQQLPQMMGKDNAVPMTVWLVPMVNFYSEAPQLMADSSTPILRKVRNTLEAIVQVQMRCNDALDDPTVNLFTEVQKKLSDFQKI-CDDHMSKLQATIAKKLFAIR--SGDEDESALLNLFEENLQSPFNIESLNMWMEFEEREINVLRSCMDILTKAKPKVIFNQGVLFKGLYDSKVKHALCYVF-TNVTKNDVFLNVLNEFLDSP------QSRPKKLRPSPKDYWYSYDDIPETM--REKAYLFRNLAKEMNNRCVHFFVTAIHNPKQEGAGI-------------HYYRESIQIIDEFTKPYMPGVESIKDRRELQWYDCELTLDPETAHQVLTLSEGNKKAVSGNTKSPTDHLEKFSHFQQVMCTKGL-SGRHYWELEWSGYVGAGVTYKGIGRKTS------TSDSSLGKNEKSWLFEYSTKSGYQQIHNSKKTRVTVSSTG------------------FKLLGVYLDWPAGTLSFYMVNKAWVTHLHTFHTKFNEAVY--PAFLIGDAQQKVNGQIKLL
Template: -----------------------------------------------------------------------------------GKLVIWINGDKGYNGLAEVGKKFEKDTGIK-----VTVEHPDKLEEKFPQVAATGDGPDII-----FWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGK----LIAYPIAV-EALSLIYNKD--LLPNP------PKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGG-------------------------------YAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKG-ETAMTINGPWAWSNIDTSKVNYGVTVLPTF-KGQPSKPF-VGVLSAGIDAASPNKELAKEFLENYLLTDEGLEAVNK--DKPLGAVALKSYEEELAKDPR--------IAATMENAQKGEIMPNI--PQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITRRVFR-----LDMF--------RELTDARR-YWVDVTLATN-NISHAVIA---EDKRQVS--SRNP--------YCTGVLGSQSITSGKHYWEVD-------------VSKKSAWILGVCAGFQSDAMYNIEQNENYQPKYGYWVIGLQEGVKYSVFQDGSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITN----HGFLIY-KFSQCSFSKPVFPYLN-PRKCTVPMTLC

4N7I
A
Unknot
34.76%
200.00%
20.00%
1.10

..Target: DILVVAALGRPFTLGMLYDARNDKLIPGFTLWEDEVIEESTLESSQPSSAFEIIASDSTDDKSSLMDIEASLKASFLGGLVEVGGSAKYLNNQKKFKNQSRVTLQYKATTSFKQLMTNLGTKHVEYSELFENIQATHVVIGILYGANAFFVFDSNKVDSTNVQEIQGQMEAVIKKIPSVEISGKASVQLTGEETDITNSFSCEFHGDFFLTTNPTTFEDAVKTYQQLPQMMGKDNAVPMTVWLVPMVNFYSEAPQLMADSSTPILRKVRNTLEAIVQVQMRCNDALDDPTVNLFTEVQKKLSDFQKICDDHMSKLQATIAKKLFAIRSGDEDESALLNLFEENLQSPFNIESLNMWMEFEEREINVLRSCMDILTKAKPKVIFNQGVLFKGLYDSKVKHALCYVFTNVTKNDVFLNVLNEFLDSPQSRPKKLRPSPKDYWYSYDDIPETMREKAYLFRNLAKEMNNRCVHFFVTAIHNPKQEGAGIHYYRESIQIIDEFTKPYMPGVESIKDRRELQWYDCELTLDPETAHQVLTLSEGNKKAVSGNTKSPTD---HLEKFS-HFQQVMCTKGLSGRHYWELE------WSGYVGAGVTYKGIGRKTSTSDSSLGKNEKSWLFEYSTKSGY--QQIHNSKKTR-VTVSSTGFKL------LGVYLDWPAGTLSFYMVNKAWVTHLHTF-HTKFNEAVYPAFLIGDAQQKVNGQIKLL
Template: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAYNEW--------KKALFKPAD------------------------------------------------------------------------------------VILDPKTADPILLVSE-DQRSVE-RAKEPQDLPDNPERFNWHYCVLGCESFISGRHYWEVEVGDRKEW----HIGVCSKNVQRK-------------GWV-KMTPENGFWTMGLTDGNKYRTLTEPRTNLKLPKPPKKVGVFLDYETGDISFY--NAVDGSHIHTFLDVSFSEALYPVFRILTLEPTAL-TICPA
Help
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

FKQLMTNLGTKHVE-YSELFENIQATHV
4B3N A Unknot 19.05% 80.95%

IK-----VTVEHPDKLEEKFPQVAATGD
4N7I A Unknot 0.00% 0.00%

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

KLIPGFTLWEDEVIEESTLESSQ
4B3N A Unknot 0.00% 0.00%

-----------------------
4N7I A Unknot 0.00% 0.00%

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

VPMVNFYSEAPQLMADSSTPI
4B3N A Unknot 26.67% 100.00%

FNLQEPYFTWPLIAADGG---
4N7I A Unknot 0.00% 0.00%

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

P----SVEISGKASVQLTGEE
4B3N A Unknot 27.27% 63.64%

PFTWDAVRYNGK----LIAYP
4N7I A Unknot 0.00% 0.00%

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

LIGDAQQKVNGQ
4B3N A Unknot 16.67% 83.33%

PYLN-PRKCTVP
4N7I A Unknot 0.00% 100.00%

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

QMMGKDNAVPM
4B3N A Unknot 20.00% 100.00%

ALDKELKAKGK
4N7I A Unknot 0.00% 0.00%

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

EYSTKSGYQQI
4B3N A Unknot 60.00% 100.00%

NYQPKYGYWVI
4N7I A Unknot 20.00% 100.00%

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

FAIR--SGDEDE
4B3N A Unknot 25.00% 100.00%

IKNKHMNADTDY
4N7I A Unknot 0.00% 0.00%

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

DSP------QSRPKKL
4B3N A Unknot 25.00% 100.00%

DKPLGAVALKSYEEEL
4N7I A Unknot 0.00% 0.00%

-------KKA

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

Sun Jul 23 14:57:10 2017	JOB CREATED : 85e1207e-7bef-4030-8a72-1e2cc49f0f53
Sun Jul 23 19:29:01 2017	STATUS CHANGED : N -> R
Sun Jul 23 19:29:01 2017	INFO : JOB STARTED AT: 2017-07-23 19:29:01.798804
Sun Jul 23 19:29:01 2017	INFO : METHOD: 1
Sun Jul 23 19:29:01 2017	INFO : Precalculated profile found...
Sun Jul 23 19:29:01 2017	INFO : Homologue pool found...
Sun Jul 23 19:29:01 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 19:29:26 2017	INFO : Starting homologue filtering...
Sun Jul 23 19:30:01 2017	INFO : Getting structures from PDB...
Sun Jul 23 19:30:09 2017	INFO : Creating modelling alignment...
Sun Jul 23 19:30:09 2017	INFO : Modelling...
Sun Jul 23 22:06:50 2017	INFO : Model 1 built
Sun Jul 23 22:06:50 2017	INFO : 2 gaps will be remodelled
Sun Jul 23 22:38:50 2017	INFO : Validating Calpha distances...
Sun Jul 23 22:38:50 2017	INFO : Model 1 distances correct: True
Sun Jul 23 22:38:50 2017	INFO : Modelling...
Mon Jul 24 00:00:06 2017	INFO : Model 2 built
Mon Jul 24 00:00:06 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 00:21:04 2017	INFO : Validating Calpha distances...
Mon Jul 24 00:21:04 2017	INFO : Model 2 distances correct: True
Mon Jul 24 00:21:04 2017	INFO : Modelling...
Mon Jul 24 02:31:22 2017	INFO : Model 3 built
Mon Jul 24 02:31:22 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 02:50:14 2017	INFO : Validating Calpha distances...
Mon Jul 24 02:50:14 2017	INFO : Model 3 distances correct: True
Mon Jul 24 02:50:14 2017	INFO : Modelling...
Mon Jul 24 05:04:10 2017	INFO : Model 4 built
Mon Jul 24 05:04:10 2017	INFO : 3 gaps will be remodelled
Mon Jul 24 05:41:32 2017	INFO : Validating Calpha distances...
Mon Jul 24 05:41:33 2017	INFO : Model 4 distances correct: False
Mon Jul 24 05:41:33 2017	INFO : Modelling...
Mon Jul 24 07:22:17 2017	INFO : Model 5 built
Mon Jul 24 07:22:17 2017	INFO : 2 gaps will be remodelled
Mon Jul 24 07:46:34 2017	INFO : Validating Calpha distances...
Mon Jul 24 07:46:34 2017	INFO : Model 5 distances correct: True
Mon Jul 24 07:47:20 2017	INFO : Finished modelling
Mon Jul 24 07:47:20 2017	STATUS CHANGED : R -> P
Mon Jul 24 07:47:20 2017	INFO : Checking topology...
Mon Jul 24 08:43:23 2017	INFO : Knot matrices done...
Mon Jul 24 08:50:24 2017	INFO : Some knots found!
Mon Jul 24 08:50:24 2017	INFO : No lassos found...
Mon Jul 24 08:50:24 2017	INFO : Finishing...
Mon Jul 24 08:50:25 2017	INFO : Job done
Mon Jul 24 08:50:25 2017	STATUS CHANGED : P -> F
Mon Jul 24 08:50:25 2017	STATUS CHANGED : F -> F
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