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Model Overview

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248

Sequence

UniProt

P31955

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

P31955: 10090.ENSMUSP000

Domain

Link to: [ InterPro ]

Model 3D Structure

	Model information:
	Modelled residue range:	135 to 177
	Based on template:	[ 2rnl ]
	Sequence Identity [%]:	81%
	Model date:	2013-05-08
	Revision date:	2013-04-01

Quaternary structure information:	[details]
Template (2rnl): MONOMER Model: MONOMER

Ligand information:	[details]
Ligands in the template: none. 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              K KNPCTAKFQN FCIHGECRYI ENLEVVTCNC HQDYFGERCG
2rnl_1#1  1     gssgssg--k knpcnaefqn fcihgeckyi ehleavtckc qqeyfgercg
                                                                      
TARGET                                     sssss s  ssssss            
2rnl_1#1                                   sssss s  ssssss            


TARGET    42    EK                                                    
2rnl_1#1  49    ek-                                                   
                                                                      
TARGET                                                                
2rnl_1#1

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

Template's ligands section 
Template without ligands. 
No ligands were included in the model.

Oligomer Modelling Log

Quaternary Structure Annotation of the Template 
 2rnl is annotated as MONOMER 
 The template structure (2rnl) 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 quaternary structure can be assumed to be identical 
 Model was succesfully built as MONOMER.

Template Selection

 - Start SMR-Pipeline for:bba72ae9a99cd5c59035cd3b07df911f on BC2-cluster at Tue May  7 22:43:01
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - Skip Template HHsearch issue
 - No template with A found
 - No template with B found
 - No template with E found
 - No template with D found
 - No template with F found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with C found
 - No template with T found
 - No template with T found
 - No template with T found
 - No template with T found
 - No template with A found
 - No template with B found
 - No template with B found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with C found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                             **************
 - building model based on 2rnlA (135-177) was successful 
 - 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:bba72ae9a99cd5c59035cd3b07df911f on BC2-cluster at Tue May  7 22:49:16
2013

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

2rnl: SOLUTION STRUCTURE OF THE EGF-LIKE DOMAIN FROM HUMAN AMPHIREGULIN
Solved by: NMR, Identified by BLAST
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-177

2rnlA

81%

1xdt: COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
Solved by: X-RAY, Resolution: 2.65A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

138-178

1xdtR

51%

1jl9: CRYSTAL STRUCTURE OF HUMAN EPIDERMAL GROWTH FACTOR
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	139-179	1jl9A	40%	>target CTAKFQNFCIH-GECRYIENLEVVTCNCHQDYFGERCGEKSM >1jl9A CPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDL [Model]
	139-181	1jl9B	41%	>target CTAKFQNFCIH-GECRYIENLEVVTCNCHQDYFGERCGEKSMKT- >1jl9B CPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWW [Model]

3njp: THE EXTRACELLULAR AND TRANSMEMBRANE DOMAIN INTERFACES IN EGROWTH FACTOR RECEPTOR SIGNALING
Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	139-181	3njpC	41%	>target -CTAKFQNFCIH-GECRYIENLEVVTCNCHQDYFGERCGEKSMKT-- >3njpC ECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWE [Model]
	139-181	3njpD	41%	>target -CTAKFQNFCIH-GECRYIENLEVVTCNCHQDYFGERCGEKSMKT-- >3njpD ECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWE [Model]

1ivo: CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN EPIDERMAL GROWTHFACTOR AND RECEPTOR EXTRACELLULAR DOMAINS.
Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	139-181	1ivoC	41%	>target -CTAKFQNFCIH-GECRYIENLEVVTCNCHQDYFGERCGEKSMKT-- >1ivoC ECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWE [Model]
	139-181	1ivoD	41%	>target -CTAKFQNFCIH-GECRYIENLEVVTCNCHQDYFGERCGEKSMKT-- >1ivoD ECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWE [Model]

1p9j: SOLUTION STRUCTURE AND DYNAMICS OF THE EGF/TGF-ALPHA CHIMERA T1E
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-181

1p9jA

40%

1nql: STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN EPIDERMAL GROWTH FACTOR (EGF) RECEPTOR IN AN INACTIVE (LOW PH) COMPLEX WITH EGF.
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-181

1nqlB

39%

2kv4: EGF
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

136-181

2kv4A

38%

1a3p: ROLE OF THE 6-20 DISULFIDE BRIDGE IN THE STRUCTURE AND ACTIVITY OF EPIDERMAL GROWTH FACTOR, NMR, 20 STRUCTURES
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

138-180

1a3pA

33%

2tgf: THE SOLUTION STRUCTURE OF HUMAN TRANSFORMING GROWTH FACTORALPHA
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-180

2tgfA

33%

1yuf: TYPE ALPHA TRANSFORMING GROWTH FACTOR, NMR, 16 MODELS WITHOUT ENERGY MINIMIZATION
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-180

1yufA

33%

3tgf: THE SOLUTION STRUCTURE OF HUMAN TRANSFORMING GROWTH FACTORALPHA
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-180

3tgfA

33%

4tgf: SOLUTION STRUCTURES OF HUMAN TRANSFORMING GROWTH FACTOR ALPHA DERIVED FROM 1*H NMR DATA
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-180

4tgfA

33%

1mox: CRYSTAL STRUCTURE OF HUMAN EPIDERMAL GROWTH FACTOR RECEPTO(RESIDUES 1-501) IN COMPLEX WITH TGF-ALPHA
Solved by: X-RAY, Resolution: 2.50A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	135-180	1moxC	33%	>target --KKNPCTAKFQNFCIHGECRYIENLEVVTCNCHQDYFGERCGEKSMK- >1moxC VSHFNDCPDSHTQFCFHGTCRFLVQEDKPACVCHSGYVGARCEHADLLA [Model]
	136-180	1moxD	33%	>target --KNPCTAKFQNFCIHGECRYIENLEVVTCNCHQDYFGERCGEKSMK- >1moxD SHFNDCPDSHTQFCFHGTCRFLVQEDKPACVCHSGYVGARCEHADLLA [Model]

1gk5: SOLUTION STRUCTURE THE MEGF/TGFALPHA44-50 CHIMERIC GROWTH FACTOR
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-180

1gk5A

33%

1yug: TYPE ALPHA TRANSFORMING GROWTH FACTOR, NMR, 15 MODELS AFTEECEPP/3 ENERGY MINIMIZATION
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-180

1yugA

33%

1eph: THREE-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE STRUCTURES OFMOUSE EPIDERMAL GROWTH FACTOR IN ACIDIC AND PHYSIOLOGICALPH SOLUTIONS
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-182

1ephA

32%

3egf: SOLUTION STRUCTURE OF MURINE EPIDERMAL GROWTH FACTOR DETERMINED BY NMR SPECTROSCOPY AND REFINED BY ENERGY MINIMIZATION WITH RESTRAINTS
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-182

3egfA

32%

1epj: THREE-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE STRUCTURES OFMOUSE EPIDERMAL GROWTH FACTOR IN ACIDIC AND PHYSIOLOGICALPH SOLUTIONS
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-182

1epjA

32%

1epi: THREE-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE STRUCTURES OFMOUSE EPIDERMAL GROWTH FACTOR IN ACIDIC AND PHYSIOLOGICALPH SOLUTIONS
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-182

1epiA

32%

1egf: SOLUTION STRUCTURE OF MURINE EPIDERMAL GROWTH FACTOR DETERMINED BY NMR SPECTROSCOPY AND REFINED BY ENERGY MINIMIZATION WITH RESTRAINTS
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-182

1egfA

32%

1epg: THREE-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE STRUCTURES OFMOUSE EPIDERMAL GROWTH FACTOR IN ACIDIC AND PHYSIOLOGICALPH SOLUTIONS
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-182

1epgA

32%

3u7u: CRYSTAL STRUCTURE OF EXTRACELLULAR REGION OF HUMAN EPIDERMFACTOR RECEPTOR 4 IN COMPLEX WITH NEUREGULIN-1 BETA
Solved by: X-RAY, Resolution: 3.03A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

136-181	3u7uG	29%	>target --KNPCTAKFQNFCIH-GECRYIENLE-VVTCNCHQDYFGERCGEKSMKT >3u7uG SHLVKCAEKEKTFCVNGGECFMVKDLPSRYLCKCPNEFTGDRCQNYVMAS [Model]
136-181	3u7uH	29%	>target ---KNPCTAKFQNFCIH-GECRYIENLE-VVTCNCHQDYFGERCGEKSMKT >3u7uH TSHLVKCAEKEKTFCVNGGECFMVKDLPSRYLCKCPNEFTGDRCQNYVMAS [Model]
136-181	3u7uI	29%	>target --KNPCTAKFQNFCIH-GECRYIENLE-VVTCNCHQDYFGERCGEKSMKT >3u7uI SHLVKCAEKEKTFCVNGGECFMVKDLPSRYLCKCPNEFTGDRCQNYVMAS [Model]
136-181	3u7uJ	29%	>target ---KNPCTAKFQNFCIH-GECRYIENLE-VVTCNCHQDYFGERCGEKSMKT >3u7uJ TSHLVKCAEKEKTFCVNGGECFMVKDLPSRYLCKCPNEFTGDRCQNYVMAS [Model]
136-180	3u7uK	30%	>target --KNPCTAKFQNFCIH-GECRYIENLE-VVTCNCHQDYFGERCGEKSMK >3u7uK SHLVKCAEKEKTFCVNGGECFMVKDLPSRYLCKCPNEFTGDRCQNYVMA [Model]
136-181	3u7uL	29%	>target ---KNPCTAKFQNFCIH-GECRYIENLE-VVTCNCHQDYFGERCGEKSMKT >3u7uL TSHLVKCAEKEKTFCVNGGECFMVKDLPSRYLCKCPNEFTGDRCQNYVMAS [Model]

1k36: NMR STRUCTURE OF HUMAN EPIREGULIN
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-179

1k36A

28%

1k37: NMR STRUCTURE OF HUMAN EPIREGULIN
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-179

1k37A

28%

3c9a: HIGH RESOLUTION CRYSTAL STRUCTURE OF ARGOS BOUND TO THE EGDOMAIN OF SPITZ
Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	137-177	3c9aD	27%	>target --NPCTAKF-QNFCIH-GECRYIEN--LEVVTCNCHQDYFGERCGEK- >3c9aD PTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKE [Model]
	137-177	3c9aC	27%	>target --NPCTAKF-QNFCIH-GECRYIEN--LEVVTCNCHQDYFGERCGEK- >3c9aC PTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKE [Model]

1hae: HEREGULIN-ALPHA EPIDERMAL GROWTH FACTOR-LIKE DOMAIN, NMR, 20 STRUCTURES
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

136-183

1haeA

27%

1haf: HEREGULIN-ALPHA EPIDERMAL GROWTH FACTOR-LIKE DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

136-183

1hafA

27%

1hrf: SOLUTION STRUCTURE OF THE EPIDERMAL GROWTH FACTOR-LIKE DOMAIN OF HEREGULIN-ALPHA, A LIGAND FOR P180ERB4
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

136-191

1hrfA

26%

1ip0: NMR STRUCTURE OF HUMAN BETACELLULIN-2
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-180

1ip0A

26%

3ca7: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE EGF DOMAIN OF SPI
Solved by: X-RAY, Resolution: 1.50A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-178

3ca7A

26%

1hre: SOLUTION STRUCTURE OF THE EPIDERMAL GROWTH FACTOR-LIKE DOMAIN OF HEREGULIN-ALPHA, A LIGAND FOR P180ERB4
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

136-191

1hreA

26%

1iox: NMR STRUCTURE OF HUMAN BETACELLULIN-2
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-180

1ioxA

26%

3ltg: CRYSTAL STRUCTURE OF THE DROSOPHILA EPIDERMAL GROWTH FACTOECTODOMAIN COMPLEXED WITH A LOW AFFINITY SPITZ MUTANT
Solved by: X-RAY, Resolution: 3.40A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-179

3ltgD

26%

3ltf: CRYSTAL STRUCTURE OF THE DROSOPHILA EPIDERMAL GROWTH FACTOECTODOMAIN IN COMPLEX WITH SPITZ
Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	137-183	3ltfB	24%	>target ---NPCTAKF-QNFCIH-GECRYIE--NLEVVTCNCHQDYFGERCGEKSMKTHS--- >3ltfB FPTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKEIDNTYLPK [Model]
	137-183	3ltfD	24%	>target ---NPCTAKF-QNFCIH-GECRYIE--NLEVVTCNCHQDYFGERCGEKSMKTHS--- >3ltfD FPTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKEIDNTYLPK [Model]

Downloads

download model.tgz

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.