SWISS-MODEL Repository - Model Details

Model Overview
Click on the bars to get more details about individual Models or experimental structures

Sequence
UniProt Q14246 EGF-like module-containing mucin-like hormone receptor-like 1 (EGF-like module receptor 1)
Homo sapiens (Human).
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

STRING
Q14246: 9606.ENSP0000031

Domain
Link to: [ InterPro ]
7tm_2
GPS
EGF_CA
EGF_CA
EGF_CA
EGF_CA
cEGF

Model 3D Structure
Model information:
Modelled residue range: 129 to 204
Based on template: [ 1emo ]  
Sequence Identity [%]: 40%
Model date: 2014-07-16
Revision date: 2014-07-15

Quaternary structure information: [details]
Template (1emo): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: CA: 2.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment

TARGET    1       SCTDINEC LTSSVCPEHS DCVNSMGSYS CSCQVGFISR NSTCEDVDEC
1emoA     2124    savdmdec kepdvc-khg qcintdgsyr cecpfgyila gnecvdtdec
                                                                      
TARGET                                sssss  sss ss   sssss   sssss   
1emoA                                 sssss  sss ss   sssss   sssss  h


TARGET    49    ADPRACPEHA TCNNTVGNYS CFCNPGFE - ------               
1emoA     2171  svgnpc-gng tcknviggfe ctceegfepg pmmtce               
                                                                      
TARGET                     sss      s ss                              
1emoA           h          sss      s ss                              



Quality


Template's ligands section
Ligands in the template: CA: 2.
Ligands in the template that will be assessed: CA2224, CA2225.
Model's ligands section
CA2224
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand A.CA2224 will not be included in the final model.
CA2224: conservation:False, RMSD:False, included: False

CA2225
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand A.CA2225 will not be included in the final model.
CA2225: conservation:False, RMSD:False, included: False

No ligands were included in the model.


Quaternary Structure Annotation of the Template
1emo is annotated as MONOMER
The template structure (1emo) was solved by NMR and does not contain any quaternary structure annotation
The template is annotated by the number of chains found in the PDB file

Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 40.789) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode

The target structure was calculated as SINGLE CHAIN


Template Selection
 - Start SMR-Pipeline for:9d934ea451abb9b6e287cef6798400f7 on BC2-cluster at Wed Jul 16 14:59:42
2014 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - No template with P found
 - No template with A found
 - No template with P found
 - No template with A found
 - No template with P found
 - No template with A found
 - No template with P found
 - No template with A found
 - No template with P found
 - No template with A found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:12): model based on new templates
 - Send 12 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -             *******
 - building model based on 1emnA (129-204) was not successful go to next best template
 -             *******
 - building model based on 1emoA (129-204) was successful 
 -         ***********
 - building model based on 2bouA (91-208) was successful 
 -                 ***********
 - building model based on 2bouA (180-302) was successful 
 -              ***********
 - building model based on 2bo2B (142-258) was successful 
 -    ******
 - building model based on 2boxA (38-108) was successful 
 -     ***********
 - building model based on 2boxA (41-159) was successful 
 -             ****************
 - building model based on 1uzjB (131-305) was successful 
 -                     **************
 - building model based on 3p5cL (218-367) was successful 
 -                                                             *****************
 - building model based on 4l6rA (664-854) was not successful go to next best template
 -                                                        **********************
 - building model based on 4k5yC (604-848) was successful 
 -        ***************
 - building model based on 1n7dA (83-250) was successful 
 -                                    ******************
 - building model based on 4dlqA (387-584) was not successful go to next best template
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:9d934ea451abb9b6e287cef6798400f7 on BC2-cluster at Wed Jul 16 15:02:56
2014 




Template Description
Match Chain SeqId

4d0f: HUMAN NOTCH1 EGF DOMAINS 11-13 MUTANT T466A
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

131-257 4d0fA 26%
[Model]
171-307 4d0fA 24%
[Model]
225-307 4d0fA 20%
[Model]
271-301 4d0fA 35%
[Model]
33-119 4d0fA 23%
[Model]
31-169 4d0fA 21%
[Model]
41-66 4d0fA 23%
[Model]
79-211 4d0fA 26%
[Model]

1toz: NMR STRUCTURE OF THE HUMAN NOTCH-1 LIGAND BINDING REGION
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

12-118 1tozA 21%
[Model]
132-255 1tozA 26%
[Model]
172-305 1tozA 24%
[Model]
225-307 1tozA 20%
[Model]
268-305 1tozA 34%
[Model]
31-168 1tozA 22%
[Model]
79-209 1tozA 27%
[Model]

2vj3: HUMAN NOTCH-1 EGFS 11-13
Solved by: X-RAY, Resolution: 2.6A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

132-256 2vj3A 27%
[Model]
172-307 2vj3A 23%
[Model]
226-307 2vj3A 22%
[Model]
269-303 2vj3A 34%
[Model]
32-119 2vj3A 24%
[Model]
31-169 2vj3A 21%
[Model]
79-210 2vj3A 27%
[Model]

2mgr: STRUCTURE OF PLASMODIUM YOELII MEROZOITE SURFACE PROTEIN 1TERMINAL DOMAIN, E28K MUTANT
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

136-204 2mgrA 19%
[Model]
32-114 2mgrA 19%
[Model]
91-113 2mgrA 25%
[Model]
180-204 2mgrA 27%
[Model]

4plo: CRYSTAL STRUCTURE OF CHICKEN NETRIN-1 (LN-LE3) IN COMPLEX DCC (FN4-5)
Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

180-307 4ploA 14%
[Model]
243-256 4ploA 21%
[Model]
295-304 4ploA 30%
[Model]
295-304 4ploA 20%
[Model]
101-123 4ploA 17%
[Model]
243-255 4ploA 23%
[Model]
157-165 4ploA 22%
[Model]
197-208 4ploA 25%
[Model]

4pln: CRYSTAL STRUCTURE OF CHICKEN NETRIN-1 (LN-LE3) COMPLEXED WNEOGENIN (FN4-5)
Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

180-307 4plnB 14%
[Model]
180-307 4plnA 14%
[Model]
243-257 4plnB 20%
[Model]
243-257 4plnA 20%
[Model]
295-303 4plnB 22%
[Model]
295-303 4plnA 22%
[Model]
241-258 4plnB 17%
[Model]
241-258 4plnA 17%
[Model]
104-121 4plnB 17%
[Model]
104-121 4plnA 17%
[Model]
187-209 4plnB 35%
[Model]
187-209 4plnA 35%
[Model]
295-304 4plnB 30%
[Model]
295-304 4plnA 30%
[Model]
157-164 4plnB 25%
[Model]
157-164 4plnA 25%
[Model]

2rqz: STRUCTURE OF SUGAR MODIFIED EPIDERMAL GROWTH FACTOR-LIKE RMOUSE NOTCH-1 RECEPTOR
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

140-168 2rqzA 21%
[Model]
173-209 2rqzA 35%
[Model]
269-306 2rqzA 21%
[Model]
32-68 2rqzA 27%
[Model]
80-118 2rqzA 26%
[Model]

4cue: HUMAN NOTCH1 EGF DOMAINS 11-13 MUTANT T466V
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

12-119 4cueA 20%
[Model]
132-257 4cueA 25%
[Model]
172-307 4cueA 23%
[Model]
226-307 4cueA 21%
[Model]
32-169 4cueA 21%
[Model]
80-211 4cueA 27%
[Model]

2rr2: STRUCTURE OF O-FUCOSYLATED EPIDERMAL GROWTH FACTOR-LIKE REMOUSE NOTCH-1 RECEPTOR
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

140-168 2rr2A 21%
[Model]
173-209 2rr2A 35%
[Model]
269-306 2rr2A 21%
[Model]
32-68 2rr2A 27%
[Model]
80-118 2rr2A 26%
[Model]

2rr0: STRUCTURE OF EPIDERMAL GROWTH FACTOR-LIKE REPEAT 12 OF MOURECEPTOR
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

140-168 2rr0A 21%
[Model]
173-209 2rr0A 35%
[Model]
269-306 2rr0A 21%
[Model]
32-68 2rr0A 27%
[Model]
80-118 2rr0A 26%
[Model]

4cuf: UMAN NOTCH1 EGF DOMAINS 11-13 MUTANT T466S
Solved by: X-RAY, Resolution: 2.29A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

12-120 4cufA 20%
[Model]
133-258 4cufA 25%
[Model]
173-308 4cufA 23%
[Model]
225-307 4cufA 20%
[Model]
32-169 4cufA 22%
[Model]
80-212 4cufA 26%
[Model]

4cud: HUMAN NOTCH1 EGF DOMAINS 11-13 MUTANT FUCOSYLATED AT T466
Solved by: X-RAY, Resolution: 1.85A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

12-119 4cudA 21%
[Model]
132-257 4cudA 25%
[Model]
173-307 4cudA 24%
[Model]
225-307 4cudA 20%
[Model]
32-169 4cudA 21%
[Model]
80-211 4cudA 26%
[Model]

4d0e: HUMAN NOTCH1 EGF DOMAINS 11-13 MUTANT GLCNAC-FUCOSE DISACCMODIFIED AT T466
Solved by: X-RAY, Resolution: 1.85A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

12-119 4d0eA 21%
[Model]
132-257 4d0eA 25%
[Model]
173-307 4d0eA 24%
[Model]
225-307 4d0eA 20%
[Model]
32-169 4d0eA 21%
[Model]
80-211 4d0eA 26%
[Model]

2mgp: STRUCTURE OF PLASMODIUM YOELII MEROZOITE SURFACE PROTEIN 1TERMINAL DOMAIN
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

136-205 2mgpA 19%
[Model]
32-114 2mgpA 19%
[Model]
91-113 2mgpA 25%
[Model]

4plm: CRYSTAL STRUCTURE OF CHICKEN NETRIN-1 (LN-LE3)
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

158-209 4plmA 23%
[Model]
180-307 4plmA 14%
[Model]
194-258 4plmA 20%
[Model]
293-340 4plmA 13%
[Model]
295-304 4plmA 20%
[Model]
241-258 4plmA 17%
[Model]
155-168 4plmA 14%
[Model]

Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.




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