Secondary structure and disorder prediction

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20

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Sequence

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R

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Y

N

P

N

S

L

L

P

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Q

M

Q

K

C

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C

N

S

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H

L

A

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G

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E

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Secondary structure

SS confidence

Disorder

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Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 1e4v chain A domain 2 Region: 2 - 32 Aligned: 22 Modelled: 31 Confidence: 7.5% Identity: 32% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1p3j chain A domain 2 Region: 2 - 32 Aligned: 22 Modelled: 31 Confidence: 7.1% Identity: 41% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 2ak3 chain A domain 2 Region: 2 - 32 Aligned: 22 Modelled: 31 Confidence: 7.0% Identity: 36% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1zin chain A domain 2 Region: 2 - 32 Aligned: 22 Modelled: 31 Confidence: 6.4% Identity: 45% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1s3g chain A domain 2 Region: 2 - 32 Aligned: 22 Modelled: 31 Confidence: 6.4% Identity: 41% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1vs6 chain 2 Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.7% Identity: 50% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli in complex with the antibiotic kasugamyin3 at 3.5a resolution. this file contains the 50s subunit of4 one 70s ribosome. the entire crystal structure contains5 two 70s ribosomes and is described in remark 400. Phyre2 PDB 3e1d chain V Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.7% Identity: 50% PDB header:ribosome Chain: V: PDB Molecule:50s ribosomal protein l34; PDBTitle: structure of the 50s subunit of e. coli ribosome in post-2 accommodation state Phyre2 PDB 1vs8 chain 2 Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.6% Identity: 50% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the bacterial ribosome from escherichia coli in2 complex with the antibiotic kasugamyin at 3.5a resolution. this file3 contains the 50s subunit of one 70s ribosome. the entire crystal4 structure contains two 70s ribosomes and is described in remark 400. Phyre2 PDB 2awb chain 2 Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.6% Identity: 50% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli at 3.5 a resolution. this file contains3 the 50s subunit of the second 70s ribosome. the entire4 crystal structure contains two 70s ribosomes and is5 described in remark 400. Phyre2 PDB 2j28 chain 2 Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.6% Identity: 50% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: model of e. coli srp bound to 70s rncs Phyre2 PDB 3e1b chain V Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.6% Identity: 50% PDB header:ribosome Chain: V: PDB Molecule:50s ribosomal protein l34; PDBTitle: structure of the 50s subunit of e. coli ribosome in pre-2 accommodation state Phyre2 PDB 2rdo chain 2 Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.6% Identity: 50% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: 50s subunit with ef-g(gdpnp) and rrf bound Phyre2 PDB 2aw4 chain 2 Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.6% Identity: 50% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli at 3.5 a resolution. this file contains3 the 50s subunit of one 70s ribosome. the entire crystal4 structure contains two 70s ribosomes and is described in5 remark 400. Phyre2 PDB 3bbx chain 2 Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.6% Identity: 50% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: the hsp15 protein fitted into the low resolution cryo-em map of the2 50s.nc-trna.hsp15 complex Phyre2 PDB 3izt chain E Region: 2 - 9 Aligned: 8 Modelled: 8 Confidence: 5.2% Identity: 50% PDB header:ribosome Chain: E: PDB Molecule:50s ribosomal protein l3; PDBTitle: structural insights into cognate vs. near-cognate discrimination2 during decoding. this entry contains the large subunit of a ribosome3 programmed with a near-cognate codon. Phyre2 1 d1e4va2 2 d1p3ja2 3 d2ak3a2 4 d1zina2 5 d1s3ga2 6 c1vs62_ 7 c3e1dV_ 8 c1vs82_ 9 c2awb2_ 10 c2j282_ 11 c3e1bV_ 12 c2rdo2_ 13 c2aw42_ 14 c3bbx2_ 15 c3izte_

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 d1e4va2 7.5 32 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 2 d1p3ja2 7.1 41 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 3 d2ak3a2 7.0 36 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 4 d1zina2 6.4 45 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 5 d1s3ga2 6.4 41 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 6 c1vs62_ 5.7 50 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli in complex with the antibiotic kasugamyin3 at 3.5a resolution. this file contains the 50s subunit of4 one 70s ribosome. the entire crystal structure contains5 two 70s ribosomes and is described in remark 400. 7 c3e1dV_ 5.7 50 PDB header:ribosome Chain: V: PDB Molecule:50s ribosomal protein l34; PDBTitle: structure of the 50s subunit of e. coli ribosome in post-2 accommodation state 8 c1vs82_ 5.6 50 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the bacterial ribosome from escherichia coli in2 complex with the antibiotic kasugamyin at 3.5a resolution. this file3 contains the 50s subunit of one 70s ribosome. the entire crystal4 structure contains two 70s ribosomes and is described in remark 400. 9 c2awb2_ 5.6 50 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli at 3.5 a resolution. this file contains3 the 50s subunit of the second 70s ribosome. the entire4 crystal structure contains two 70s ribosomes and is5 described in remark 400. 10 c2j282_ 5.6 50 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: model of e. coli srp bound to 70s rncs 11 c3e1bV_ 5.6 50 PDB header:ribosome Chain: V: PDB Molecule:50s ribosomal protein l34; PDBTitle: structure of the 50s subunit of e. coli ribosome in pre-2 accommodation state 12 c2rdo2_ 5.6 50 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: 50s subunit with ef-g(gdpnp) and rrf bound 13 c2aw42_ 5.6 50 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli at 3.5 a resolution. this file contains3 the 50s subunit of one 70s ribosome. the entire crystal4 structure contains two 70s ribosomes and is described in5 remark 400. 14 c3bbx2_ 5.6 50 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: the hsp15 protein fitted into the low resolution cryo-em map of the2 50s.nc-trna.hsp15 complex 15 c3izte_ 5.2 50 PDB header:ribosome Chain: E: PDB Molecule:50s ribosomal protein l3; PDBTitle: structural insights into cognate vs. near-cognate discrimination2 during decoding. this entry contains the large subunit of a ribosome3 programmed with a near-cognate codon.

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0