SWISS-MODEL Repository
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
| UniProt | O18276 |
Database: TrEMBL (Unreviewed)  |
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Domain
Model 3D Structure
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Template Links:
[ RCSB ]
[ PDBe ]
[ SCOP ]
[ CATH ]
display model: in [ AstexViewer ] download model: as [ pdb ] - as [ Deepview project ] |
Alignment
TARGET 1 ARVALG ITTVLTMTTI STGVRQSLPR ISYVKSIDIY LVMCFVFVFA
1vry_1#2 65533 lp--arvglg ittvltlttq ssgsraslpk vsyvkaidiw lavcllfvfs
TARGET hhhhh hhhhhhhhhh hh hhhhhh h hhhhhhhhhh
1vry_1#2 hhhhhh hhhhhhhhhh hh hhhhhh h hhhhhhhhhh
TARGET 47 ALLEYAAVNY --
1vry_1#2 45 alleyaavnf vsr
TARGET hhhhhhhhhh
1vry_1#2 hhhhhhhhhh h
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1vry is annotated as MONOMER
The template structure (1vry) 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:a8dc46ddd09bd518fb70bdf75d3e7dab on BC2-cluster at Mon May 6 19:47:01
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...
FATAL - No md5 found in hash for: 4hfhA
FATAL - No md5 found in hash for: 4hfhD
FATAL - No md5 found in hash for: 4hfhC
FATAL - No md5 found in hash for: 4hfhB
FATAL - No md5 found in hash for: 4hfhE
FATAL - No md5 found in hash for: 4hfbB
FATAL - No md5 found in hash for: 4hfbE
FATAL - No md5 found in hash for: 4hfbA
FATAL - No md5 found in hash for: 4hfbD
FATAL - No md5 found in hash for: 4hfbC
FATAL - No md5 found in hash for: 4hfeE
FATAL - No md5 found in hash for: 4hfeA
FATAL - No md5 found in hash for: 4hfeD
FATAL - No md5 found in hash for: 4hfeC
FATAL - No md5 found in hash for: 4hfeB
FATAL - No md5 found in hash for: 4hfcD
FATAL - No md5 found in hash for: 4hfcC
FATAL - No md5 found in hash for: 4hfcB
FATAL - No md5 found in hash for: 4hfcE
FATAL - No md5 found in hash for: 4hfcA
FATAL - No md5 found in hash for: 4hfdC
FATAL - No md5 found in hash for: 4hfdB
FATAL - No md5 found in hash for: 4hfdE
FATAL - No md5 found in hash for: 4hfdA
FATAL - No md5 found in hash for: 4hfdD
- Generate new template library
- Run template selection against modified template library
- Summarize templates:
- Skip Template HHsearch issue
- Skipping oligomeric state prediction due to too many templates for cluster: 76_348
- Skipping oligomeric state prediction due to too many templates for cluster: 52_258
- Skip Template HHsearch issue
- Warning: Oligomer Prediction was not successfull!
- Warning: clustersMergedFile not found
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:2): model based on new templates
- Send 2 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ********
- building model based on 1vryA (292-347) was successful
- *******************************************
- building model based on 3rhwE (55-347) 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:a8dc46ddd09bd518fb70bdf75d3e7dab on BC2-cluster at Mon May 6 19:59:48
2013
Template Search
| Template Description |
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1vry: SECOND AND THIRD TRANSMEMBRANE DOMAINS OF THE ALPHA-1 SUBUNIT OF HUMAN GLYCINE RECEPTOR Solved by: NMR, Identified by BLAST |
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3rhw: C. ELEGANS GLUTAMATE-GATED CHLORIDE CHANNEL (GLUCL) IN COMFAB AND IVERMECTIN Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH |
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3rif: C. ELEGANS GLUTAMATE-GATED CHLORIDE CHANNEL (GLUCL) IN COMFAB, IVERMECTIN AND GLUTAMATE. Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH |
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3ria: C. ELEGANS GLUTAMATE-GATED CHLORIDE CHANNEL (GLUCL) IN COMFAB, IVERMECTIN AND IODIDE. Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH |
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3ri5: C. ELEGANS GLUTAMATE-GATED CHLORIDE CHANNEL (GLUCL) IN COMFAB, IVERMECTIN AND PICROTOXIN Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH |
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2k58: NMR STRUCTURES OF THE FIRST TRANSMEMBRANE DOMAIN OF THE NEURONAL ACETYLCHOLINE RECEPTOR BETA 2 SUBUNIT Solved by: NMR, Identified by HHSEARCH |
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4aq9: GATING MOVEMENT IN ACETYLCHOLINE RECEPTOR ANALYSED BY TIME-RESOLVED ELECTRON CRYO-MICROSCOPY (OPEN CLASS) Solved by: X-RAY, Resolution: 6.20A, Identified by HHSEARCH |
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4aq5: GATING MOVEMENT IN ACETYLCHOLINE RECEPTOR ANALYSED BY TIMERESOLVED ELECTRON CRYO-MICROSCOPY (CLOSED CLASS) Solved by: X-RAY, Resolution: 6.20A, Identified by HHSEARCH |
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2bg9: REFINED STRUCTURE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR AT 4A RESOLUTION. Solved by: X-RAY, Resolution: 6.20A, Identified by HHSEARCH |
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2ksr: NMR STRUCTURES OF TM DOMAIN OF THE N-ACETYLCHOLINE RECEPTO Solved by: NMR, Identified by HHSEARCH |
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4a98: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC) IN COMPLEX WITH BROMOFLURAZEPAM Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH |
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3rqu: CRYSTAL STRUCTURE OF A PROKARYOTIC PENTAMERIC LIGAND-GATEDCHANNEL, ELIC Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH |
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3uq4: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FCHRYSANTHEMI (ELIC) MUTANT F247L (F16L) Solved by: X-RAY, Resolution: 3.50A, Identified by HHSEARCH |
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2yn6: PENTAMERIC LIGAND-GATED ION CHANNEL ELIC IN COMPLEX WITH BARIUM Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH |
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3zkr: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC) IN COMPLEX WITH BROMOFOR Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH |
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4a97: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC) IN COMPLEX WITH ZOPICLON Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH |
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2lly: NMR STRUCTURES OF THE TRANSMEMBRANE DOMAINS OF THE NACHR A Solved by: NMR, Identified by HHSEARCH |
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3rqw: CRYSTAL STRUCTURE OF ACETYLCHOLINE BOUND TO A PROKARYOTIC LIGAND-GATED ION CHANNEL, ELIC Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH |
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2yoe: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC) IN COMPLEX WITH GABA ANDFLURAZEPAM Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH |
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3uq7: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FCHRYSANTHEMI (ELIC) MUTANT L240S F247L (L9S F16L) IN PRESMM CYSTEAMINE Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH |
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2yks: PENTAMERIC LIGAND GATED ION CHANNEL ELIC MUTANT F246A Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH |
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2lm2: NMR STRUCTURES OF THE TRANSMEMBRANE DOMAINS OF THE ACHR B2 Solved by: NMR, Identified by HHSEARCH |
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1oed: STRUCTURE OF ACETYLCHOLINE RECEPTOR PORE FROM ELECTRON IMAGES Solved by: X-RAY, Resolution: 4.00A, Identified by HHSEARCH |
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2vl0: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC) Solved by: X-RAY, Resolution: 3.3A, Identified by HHSEARCH |
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3uq5: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FCHRYSANTHEMI (ELIC) MUTANT L240A F247L (L9A F16L) IN THE 10 MM CYSTEAMINE Solved by: X-RAY, Resolution: 4.20A, Identified by HHSEARCH |
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3lsv: STRUCTURE OF THE A237F MUTANT OF THE PENTAMERIC LIGAND GATCHANNEL FROM GLOEOBACTER VIOLACEUS Solved by: X-RAY, Resolution: 3.50A, Identified by HHSEARCH |
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4ilb: THE PENTAMERIC LIGAND-GATED ION CHANNEL GLIC A237F IN COMPRUBIDIUM Solved by: X-RAY, Resolution: 3.50A, Identified by HHSEARCH |
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2xq8: PENTAMERIC LIGAND GATED ION CHANNEL GLIC IN COMPLEX WITH ZION (ZN2+) Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH |
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4il9: THE PENTAMERIC LIGAND-GATED ION CHANNEL GLIC A237F IN COMPBROMIDE Solved by: X-RAY, Resolution: 3.50A, Identified by HHSEARCH |
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3p4w: STRUCTURE OF DESFLURANE BOUND TO A PENTAMERIC LIGAND-GATEDCHANNEL, GLIC Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH |
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2xq5: PENTAMERIC LIGAND GATED ION CHANNEL GLIC IN COMPLEX WITH TETRAETHYLARSONIUM (TEAS) Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH |
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3uu3: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL LOOP2-20' OXIIN A LOCALLY-CLOSED CONFORMATION (LC1 SUBTYPE) Solved by: X-RAY, Resolution: 3.15A, Identified by HHSEARCH |
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3ei0: STRUCTURE OF THE E221A MUTANT OF THE GLOEBACTER VIOLACEUS PENTAMERIC LIGAND GATED ION CHANNNEL (GLIC) Solved by: X-RAY, Resolution: 3.50A, Identified by HHSEARCH |
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3tlt: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL H11'F MUTANT LOCALLY-CLOSED CONFORMATION (LC1 SUBTYPE) Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH |
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2xqa: PENTAMERIC LIGAND GATED ION CHANNEL GLIC IN COMPLEX WITH TETRABUTYLANTIMONY (TBSB) Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH |
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2xq9: PENTAMERIC LIGAND GATED ION CHANNEL GLIC MUTANT E221A IN CTETRAETHYLARSONIUM (TEAS) Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH |
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2xq3: PENTAMERIC LIGAND GATED ION CHANNEL GLIC IN COMPLEX WITH BR-LIDOCAINE Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH |
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4f8h: X-RAY STRUCTURE OF THE ANESTHETIC KETAMINE BOUND TO THE GLPENTAMERIC LIGAND-GATED ION CHANNEL Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH |
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3p50: STRUCTURE OF PROPOFOL BOUND TO A PENTAMERIC LIGAND-GATED IGLIC Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH |
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4ilc: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL IN COMPLEX WI Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH |
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4il4: THE PENTAMERIC LIGAND-GATED ION CHANNEL GLIC IN COMPLEX WI Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH |
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4hfi: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL AT 2.4 A RESO Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH |
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2xq6: PENTAMERIC LIGAND GATED ION CHANNEL GLIC IN COMPLEX WITH CION (CS+) Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH |
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2xq4: PENTAMERIC LIGAND GATED ION CHANNEL GLIC IN COMPLEX WITH TETRAMETHYLARSONIUM (TMAS) Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH |
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3tlw: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL LOOP2-21' OXIIN A LOCALLY-CLOSED CONFORMATION (LC2 SUBTYPE) Solved by: X-RAY, Resolution: 3.05A, Identified by HHSEARCH |
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4ila: THE PENTAMERIC LIGAND-GATED ION CHANNEL GLIC A237F IN COMPCESIUM Solved by: X-RAY, Resolution: 3.50A, Identified by HHSEARCH |
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3tlu: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL LOOP2-24' OXIIN A LOCALLY-CLOSED CONFORMATION (LC1 SUBTYPE) Solved by: X-RAY, Resolution: 3.25A, Identified by HHSEARCH |
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3tls: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL E19'P MUTANT LOCALLY-CLOSED CONFORMATION (LC2 SUBTYPE) Solved by: X-RAY, Resolution: 3.20A, Identified by HHSEARCH |
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2xq7: PENTAMERIC LIGAND GATED ION CHANNEL GLIC IN COMPLEX WITH CION (CD2+) Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH |
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3uu8: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL LOOP2-24' MUTIN SOLUTION Solved by: X-RAY, Resolution: 3.25A, Identified by HHSEARCH |
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3uu4: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL LOOP2-21' MUTIN THE CRYSTAL IN A LOCALLY-CLOSED CONFORMATION (LC1 SUBT Solved by: X-RAY, Resolution: 3.05A, Identified by HHSEARCH |
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3uub: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL LOOP2-21' MUTIN SOLUTION Solved by: X-RAY, Resolution: 3.05A, Identified by HHSEARCH |
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3uu5: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL LOOP2-20' MUTIN SOLUTION Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH |
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3eam: AN OPEN-PORE STRUCTURE OF A BACTERIAL PENTAMERIC LIGAND- GATED ION CHANNEL Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH |
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3ehz: X-RAY STRUCTURE OF THE PENTAMERIC LIGAND GATED ION CHANNELOF GLOEBACTER VIOLACEUS (GLIC) IN A PRESUMPTIVE OPEN CONFORMATION Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH |
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2y7y: APLYSIA CALIFORNICA ACHBP IN APO STATE Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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4dbm: APLYSIA CALIFORNICA-ACHBP IN COMPLEX WITH TRIAZOLE 18 Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH |
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3uu6: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL LOOP2-22' MUTIN SOLUTION Solved by: X-RAY, Resolution: 2.98A, Identified by HHSEARCH |
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2byn: CRYSTAL STRUCTURE OF APO ACHBP FROM APLYSIA CALIFORNICA Solved by: X-RAY, Resolution: 2.02A, Identified by HHSEARCH |
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2qc1: CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE NICOTINIC ACETYLCHOLINE RECEPTOR 1 SUBUNIT BOUND TO ALPHABUNGAROTOXIN AT 1.9 A RESOLUTION Solved by: X-RAY, Resolution: 1.94A, Identified by HHSEARCH |
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3pmz: CRYSTAL STRUCTURE OF THE COMPLEX OF ACETYLCHOLINE BINDING D-TUBOCURARINE Solved by: X-RAY, Resolution: 2.44A, Identified by HHSEARCH |
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4aod: BIOMPHALARIA GLABRATA ACETYLCHOLINE-BINDING PROTEIN TYPE 1 Solved by: X-RAY, Resolution: 6.00A, Identified by HHSEARCH |
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3tlv: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL LOOP2-22' OXIIN A LOCALLY-CLOSED CONFORMATION (LC3 SUBTYPE) Solved by: X-RAY, Resolution: 2.98A, Identified by HHSEARCH |
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2y54: FRAGMENT GROWING INDUCES CONFORMATIONAL CHANGES IN ACETYLCBINDING PROTEIN: A STRUCTURAL AND THERMODYNAMIC ANALYSIS 1) Solved by: X-RAY, Resolution: 3.65A, Identified by HHSEARCH |
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2wnj: CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH DMXBA Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH |
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