GapRepairer

Models

Number of gaps:2

Gap lengths: 11, 11

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap	2nd gap
Model 1	Non-trivial	-94373	-1916	-1394
Model 2	Non-trivial	-94470	-1892	-1474
Model 3	Non-trivial	-94249	-1823	-1212
Model 4	Non-trivial	-94320	-1790	-1389
Model 5	Non-trivial	-94531	-1733	-1626
Colour the base model according to the B-factor (lowest to highest)					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	116-300	300-565	--	--
	Lasso	L_+2C	--	--	101-295
Model 2	Slipknot	S 3₁	116-300	300-565	--	--
	Lasso	L_+2C	--	--	101-295
Model 3	Slipknot	S 3₁	116-300	300-565	--	--
	Lasso	L_+2C	--	--	101-295
Model 4	Slipknot	S 3₁	116-300	300-565	--	--
	Lasso	L_+2C	--	--	101-295
Model 5	Slipknot	S 3₁	116-300	300-565	--	--
	Lasso	L_+2C	--	--	101-295
							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.

Knotting fingerprint thumbnails
Lasso thumbnails

Knot help

Lasso help

Model 1

Model 2

Model 3

Model 4

Model 5

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.

Templates (similarity across the whole protein) Help

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	96.77%	163.64%	163.64%	0.63	..Target: -----GSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKXFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDDKVEPKNKLEEFNKRLHTKGSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE Template: WTNTSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIRVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRPKIPNNLKYDPKAIIANLTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDLHLLVERRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTLPEEVSRPNYPGIMYLQSDFDLGCTCDD----KNKLEELNKRLHTKGSTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWTYFQRVLVKKYASERNGVNVISGPIFDYNYNGLRDIEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE

Templates (similarity to the largest gap - 11 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	RKPLDVYKKPSGKCFFQ
3NKM	A	S +3₁	100.00%	100.00%	RKPLDVYKKPSGKCFFQ

Templates (similarity to the 2nd largest gap - 11 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	CTCDDKVEPKNKLEEFN
3NKM	A	S +3₁	63.64%	63.64%	CTCDD----KNKLEELN

Download Files Models Similarity profile Modelling alignment Raw knot fingerprint matrices: Model_1 Model_2 Model_3 Model_4 Model_5

Job Log

Fri Dec  1 09:35:16 2017	JOB CREATED : ee6c9352-ee1e-487a-b5ca-11635de93adf
Fri Dec  1 09:36:02 2017	STATUS CHANGED : N -> R
Fri Dec  1 09:36:02 2017	INFO : JOB STARTED AT: 2017-12-01 09:36:02.149751
Fri Dec  1 09:36:02 2017	INFO : METHOD: 1
Fri Dec  1 09:36:02 2017	INFO : Precalculated profile found...
Fri Dec  1 09:36:02 2017	INFO : Homologue pool found...
Fri Dec  1 09:36:02 2017	INFO : Verifying structure sequences of homologues...
Fri Dec  1 09:38:41 2017	INFO : Starting homologue filtering...
Fri Dec  1 09:41:03 2017	INFO : Getting structures from PDB...
Fri Dec  1 09:41:40 2017	INFO : Creating modelling alignment...
Fri Dec  1 09:41:40 2017	INFO : Modelling...
Fri Dec  1 09:55:46 2017	INFO : Model 1 built
Fri Dec  1 09:55:46 2017	INFO : Validating Calpha distances...
Fri Dec  1 09:55:46 2017	INFO : Model 1 distances correct: True
Fri Dec  1 09:55:46 2017	INFO : Modelling...
Fri Dec  1 10:11:47 2017	INFO : Model 2 built
Fri Dec  1 10:11:47 2017	INFO : Validating Calpha distances...
Fri Dec  1 10:11:47 2017	INFO : Model 2 distances correct: True
Fri Dec  1 10:11:47 2017	INFO : Modelling...
Fri Dec  1 10:25:13 2017	INFO : Model 3 built
Fri Dec  1 10:25:13 2017	INFO : Validating Calpha distances...
Fri Dec  1 10:25:13 2017	INFO : Model 3 distances correct: True
Fri Dec  1 10:25:13 2017	INFO : Modelling...
Fri Dec  1 11:10:43 2017	INFO : Model 4 built
Fri Dec  1 11:10:43 2017	INFO : Validating Calpha distances...
Fri Dec  1 11:10:43 2017	INFO : Model 4 distances correct: True
Fri Dec  1 11:10:43 2017	INFO : Modelling...
Fri Dec  1 11:32:43 2017	INFO : Model 5 built
Fri Dec  1 11:32:43 2017	INFO : Validating Calpha distances...
Fri Dec  1 11:32:43 2017	INFO : Model 5 distances correct: True
Fri Dec  1 11:35:26 2017	INFO : Finished modelling
Fri Dec  1 11:35:26 2017	STATUS CHANGED : R -> P
Fri Dec  1 11:35:26 2017	INFO : Checking topology...
Fri Dec  1 11:55:35 2017	INFO : Knot matrices done...
Fri Dec  1 12:10:48 2017	INFO : Some knots found!
Fri Dec  1 12:13:17 2017	INFO : Some lassos found!
Fri Dec  1 12:13:17 2017	INFO : Finishing...
Fri Dec  1 12:13:17 2017	STATUS CHANGED : P -> E
Fri Dec  1 12:13:17 2017	ERROR : Error while finishing
Fri Dec  1 12:13:17 2017	STATUS CHANGED : E -> F

5IJS chain A