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SWISS-MODEL Repository - Model Details

Model Overview

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236

Sequence

UniProt

P50553

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

P50553: 9606.ENSP0000026

Domain

Link to: [ InterPro ]

HLH

Model 3D Structure

	Model information:
	Modelled residue range:	120 to 175
	Based on template:	[ 2ql2 ]
	Sequence Identity [%]:	42%
	Model date:	2013-04-24
	Revision date:	2013-04-01

Quaternary structure information:	[details]
Template (2ql2): HETERO DIMER Model built :SINGLE CHAIN

Ligand information:	[details]
Ligands in the template: DC: 1, DT: 1. 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        VARRNER ERNRVKLVNL GFATLREHVP NGAANKKMSK VETLRSAVEY
2ql2D     102   r--rmkanar ernrmhglna aldnlrkvvp cysktqklsk ietlrlakny
                                                                      
TARGET              hhhhhh hhhhhhhhhh hhhhhhhh            h hhhhhhhhhh
2ql2D               hhhhhh hhhhhhhhhh hhhhhhhh            h hhhhhhhhhh


TARGET    48    IRALQQLLD                                             
2ql2D     150   iwalseilr-                                            
                                                                      
TARGET          hhhhhhhh                                              
2ql2D           hhhhhhhh

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

Template's ligands section 
Ligands in the template: DC: 1, DT: 1. 
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page. 
No ligands were included in the model.

Oligomer Modelling Log

Quaternary Structure Annotation of the Template
2ql2 is annotated as HETERO DIMER
The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry
The following biological unit was used to build the template structure: 2ql2.pdb2.gz

Quaternary Structure Modelling of the Target Protein
2ql2_2

Template Selection

 - Start SMR-Pipeline for:330679831a7d599083df959fed439d4b on BC2-cluster at Tue Apr 23 23:55:39
2013 


 - Found BLAST templates: 2
 - 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 modfied template library 
 - Summarize templates: 
 - No template with B found
 - No template with A found
 - No template with A found
 - No template with B found
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                          *******************
 - building model based on 2ql2D (120-175) 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:330679831a7d599083df959fed439d4b on BC2-cluster at Wed Apr 24 00:32:34
2013

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

4aya: CRYSTAL STRUCTURE OF ID2 HLH HOMODIMER AT 2.1A RESOLUTION
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	128-178	4ayaA	37%	>target ---RNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD----- >4ayaA DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLKPSFL [Model]
	131-177	4ayaB	40%	>target -VKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEH >4ayaB LLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSH [Model]

1mdy: CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

117-176	1mdyB	37%	>target ---PAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDE >1mdyB TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIEGLQALLRD [Model]
117-176	1mdyA	37%	>target ---------PAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDE >1mdyA MELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIEGLQALLRD [Model]
117-176	1mdyD	37%	>target ---PAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDE >1mdyD TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIEGLQALLRD [Model]
117-176	1mdyC	37%	>target ---PAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDE >1mdyC TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSN-PNQRLPKVEILRNAIRYIEGLQALLRD [Model]

1nkp: CRYSTAL STRUCTURE OF MYC-MAX RECOGNIZING DNA
Solved by: X-RAY, Resolution: 1.80A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

116-178	1nkpA	27%	>target --QPAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD----------------------- >1nkpA GHMNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQLGGC [Model]
119-176	1nkpB	29%	>target -AVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDE------------------------- >1nkpB DKRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRALGGC [Model]
117-178	1nkpD	27%	>target -PAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD-------------------- >1nkpD MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQL [Model]
121-177	1nkpE	32%	>target -ARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEH------------------------ >1nkpE RAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRALGGC [Model]

2lfh: SOLUTION NMR STRUCTURE OF THE HELIX-LOOP-HELIX DOMAIN OF HPROTEIN, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	124-172	2lfhA	31%	>target ------------------NERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQ- >2lfhA MGHHHHHHSHMGGGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQVV [Model]
	124-172	2lfhB	31%	>target ------------------NERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQ- >2lfhB MGHHHHHHSHMGGGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQVV [Model]

1nlw: CRYSTAL STRUCTURE OF MAD-MAX RECOGNIZING DNA
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

120-178	1nlwA	24%	>target -VARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD------------------- >1nlwA SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLEK [Model]
120-178	1nlwB	31%	>target -VARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD----------------- >1nlwB KRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQV [Model]
120-178	1nlwD	24%	>target -VARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD----------------- >1nlwD SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQL [Model]
122-178	1nlwE	30%	>target -RRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD----------------- >1nlwE AHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQV [Model]

1an2: RECOGNITION BY MAX OF ITS COGNATE DNA THROUGH A DIMERIC B/HLH/Z DOMAIN
Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

119-178

1an2A

30%

2ql2: CRYSTAL STRUCTURE OF THE BASIC-HELIX-LOOP-HELIX DOMAINS OFTHE HETERODIMER E47/NEUROD1 BOUND TO DNA
Solved by: X-RAY, Resolution: 2.50A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

119-175	2ql2B	42%	>target -AVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLD- >2ql2B SRRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILRS [Model]
120-176	2ql2A	32%	>target -VARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDE >2ql2A RRMANNARERVRVRDINEAFRELGRMCQL--HLKAQTKLLILQQAVQVILGLEQQVRE [Model]
120-177	2ql2C	29%	>target -VARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEH >2ql2C RRMANNARERVRVRDINEAFRELGRMCQ-LHLKSDQTKLLILQQAVQVILGLEQQVRER [Model]
120-175	2ql2D	43%	>target -VARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLD >2ql2D RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR [Model]

1hlo: THE CRYSTAL STRUCTURE OF AN INTACT HUMAN MAX-DNA COMPLEX: NEW INSIGHTS INTO MECHANISMS OF TRANSCRIPTIONAL CONTROL
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	117-178	1hloB	29%	>target --PAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD---------- >1hloB SDADKRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQN [Model]
	116-179	1hloA	28%	>target --------QPAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDA--------- >1hloA NDDIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQN [Model]

1r05: SOLUTION STRUCTURE OF MAX B-HLH-LZ
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	118-178	1r05B	28%	>target --AAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD------------------------- >1r05B MADKRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKVHTLQQDIDDLKRQNALLEQQVRALEGSGC [Model]
	118-178	1r05A	28%	>target --AAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD------------------------- >1r05A MADKRAHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKVHTLQQDIDDLKRQNALLEQQVRALEGSGC [Model]

3u5v: CRYSTAL STRUCTURE OF MAX-E47
Solved by: X-RAY, Resolution: 1.70A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

123-178

3u5vA

28%

1an4: STRUCTURE AND FUNCTION OF THE B/HLH/Z DOMAIN OF USF
Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	118-174	1an4B	28%	>target ---AAVARRNERERNRVKLVNLGFATLREHVPNGA---ANKKMSKVETLRSAVEYIRALQQLL-- >1an4B MDEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR [Model]
	118-174	1an4A	28%	>target ---AAVARRNERERNRVKLVNLGFATLREHVPNGA---ANKKMSKVETLRSAVEYIRALQQLL-- >1an4A MDEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR [Model]

1ukl: CRYSTAL STRUCTURE OF IMPORTIN-BETA AND SREBP-2 COMPLEX
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

131-181	1uklD	27%	>target VKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDAVS------------ >1uklD RSSINDKIIELKDLVMG--TDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKNKL [Model]
131-181	1uklC	27%	>target VKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDAVS------------ >1uklC RSSINDKIIELKDLVMG--TDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKNKL [Model]
131-181	1uklF	27%	>target VKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDAVS------------ >1uklF RSSINDKIIELKDLVMG--TDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKNKL [Model]
131-181	1uklE	27%	>target VKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDAVS------------ >1uklE RSSINDKIIELKDLVMG--TDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKNKL [Model]

4ati: MITF:M-BOX COMPLEX
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	118-177	4atiB	25%	>target -AAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEH---------- >4atiB RQKKDNHNLIERRRRFNINDRIKELGTLIPKSDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQKKL [Model]
	123-178	4atiA	27%	>target RNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD---- >4atiA HNLIERRRRFNINDRIKELGTLIPKS---MRWNKGTILKASVDYIRKLQREQQRAKDLEN [Model]

4atk: MITF:E-BOX COMPLEX
Solved by: X-RAY, Resolution: 2.95A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	122-177	4atkA	27%	>target -RRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEH---- >4atkA DNHNLIERRRRFNINDRIKELGTLIPK-DPDMRWNKGTILKASVDYIRKLQREQQRAKDLE [Model]
	120-175	4atkB	26%	>target -VARRNERERNRVKLVNLGFATLREHVPNGA-ANKKMSKVETLRSAVEYIRALQQLLD-- >4atkB KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRA [Model]

4f3l: CRYSTAL STRUCTURE OF THE HETERODIMERIC CLOCK:BMAL1 TRANSCRACTIVATOR COMPLEX
Solved by: X-RAY, Resolution: 2.27A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

118-173

4f3lB

25%

[Model]

4h10: INTERMOLECULAR RECOGNITION REVEALED BY THE COMPLEX STRUCTUCLOCK-BMAL1 BASIC HELIX-LOOP-HELIX DOMAINS WITH E-BOX DNA
Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

118-172

4h10A

25%

4ath: MITF APO STRUCTURE
Solved by: X-RAY, Resolution: 1.95A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	131-173	4athB	25%	>target ---VKLVNLGFATLREHVPNG-AANKKMSKVETLRSAVEYIRALQQL----------------------------------- >4athB GAMRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQKKLEHANRHLLLRVQELEMQARAH [Model]
	131-173	4athA	25%	>target -VKLVNLGFATLREHVPNG-AANKKMSKVETLRSAVEYIRALQQL----------------------------------- >4athA MRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQKKLEHANRHLLLRVQELEMQARAH [Model]

1am9: HUMAN SREBP-1A BOUND TO LDL RECEPTOR PROMOTER
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

116-179	1am9C	23%	>target --QPAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDA------------------ >1am9C QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLKDL [Model]
117-178	1am9D	24%	>target ---PAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD------------- >1am9D QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKS [Model]
117-179	1am9A	24%	>target ---PAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDA---------------- >1am9A QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGT--EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSKSLK [Model]
117-178	1am9B	24%	>target --PAAVARRNERERNRVKLVNLGFATLREHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHD------------- >1am9B SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVG--TEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKS [Model]

1a0a: PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	119-175	1a0aB	23%	>target -AVARRNERERNRVKLVNLGFATLREHVPNG----AANKKMSKVETLRSAVEYIRALQQLLD- >1a0aB MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST [Model]
	119-175	1a0aA	23%	>target -AVARRNERERNRVKLVNLGFATLREHVPNG----AANKKMSKVETLRSAVEYIRALQQLLD- >1a0aA MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST [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.