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(-) Description

Title :  SINDBIS VIRUS CAPSID PROTEIN (114-264)
 
Authors :  S. Lee, R. J. Kuhn, M. G. Rossmann
Date :  12 Jan 98  (Deposition) - 29 Apr 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Coat Protein, Sindbis, Virus, Proteinase, Alphavirus, Capsid, Dioxane, Viral Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Lee, R. J. Kuhn, M. G. Rossmann
Probing The Potential Glycoprotein Binding Site Of Sindbis Virus Capsid Protein With Dioxane And Model Building.
Proteins V. 33 311 1998 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - SINDBIS VIRUS CAPSID PROTEIN
    Cell LineBL21
    ChainsA, B, C, D
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidBL21
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System VectorPET11A
    FragmentC-TERMINAL DOMAIN
    GenePOTENTIAL
    Organism ScientificSINDBIS VIRUS
    Organism Taxid11034
    StrainSA-AR 86
    SynonymSINDBIS VIRUS CORE PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1DIO5Ligand/Ion1,4-DIETHYLENE DIOXIDE
2FOR4Mod. ResidueFORMYL GROUP
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DIO1Ligand/Ion1,4-DIETHYLENE DIOXIDE
2FOR1Mod. ResidueFORMYL GROUP
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
2FOR1Mod. ResidueFORMYL GROUP
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1DIO1Ligand/Ion1,4-DIETHYLENE DIOXIDE
2FOR1Mod. ResidueFORMYL GROUP
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1DIO1Ligand/Ion1,4-DIETHYLENE DIOXIDE
2FOR1Mod. ResidueFORMYL GROUP

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:113 , ARG A:114BINDING SITE FOR RESIDUE FOR A 112
2AC2SOFTWAREMET B:113 , VAL C:125BINDING SITE FOR RESIDUE FOR B 112
3AC3SOFTWAREMET C:113BINDING SITE FOR RESIDUE FOR C 112
4AC4SOFTWAREMET D:113BINDING SITE FOR RESIDUE FOR D 112
5AC5SOFTWAREMET A:132 , GLU A:133 , ARG A:207 , TRP A:247 , HOH A:396BINDING SITE FOR RESIDUE DIO A 1
6AC6SOFTWARETRP B:247 , HOH B:369BINDING SITE FOR RESIDUE DIO B 2
7AC7SOFTWAREHOH A:306 , TYR B:162 , TRP B:247 , THR B:253 , HOH B:369BINDING SITE FOR RESIDUE DIO B 22
8AC8SOFTWAREGLU C:133 , LYS C:135 , MET C:137BINDING SITE FOR RESIDUE DIO C 3
9AC9SOFTWAREMET D:132 , ARG D:207 , TRP D:247 , HOH D:372BINDING SITE FOR RESIDUE DIO D 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WYK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WYK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WYK)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHAVIRUS_CPPS51690 Alphavirus core protein (CP) domain profile.POLS_SINDO114-264
 
 
 
  4A:114-264
B:114-264
C:114-264
D:114-264
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHAVIRUS_CPPS51690 Alphavirus core protein (CP) domain profile.POLS_SINDO114-264
 
 
 
  1A:114-264
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHAVIRUS_CPPS51690 Alphavirus core protein (CP) domain profile.POLS_SINDO114-264
 
 
 
  1-
B:114-264
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHAVIRUS_CPPS51690 Alphavirus core protein (CP) domain profile.POLS_SINDO114-264
 
 
 
  1-
-
C:114-264
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHAVIRUS_CPPS51690 Alphavirus core protein (CP) domain profile.POLS_SINDO114-264
 
 
 
  1-
-
-
D:114-264

(-) Exons   (0, 0)

(no "Exon" information available for 1WYK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:152
 aligned with POLS_SINDO | P27285 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:152
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  
           POLS_SINDO   113 DRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW 264
               SCOP domains d1wyka_ A: Viral capsid protein                                                                                                                          SCOP domains
               CATH domains -1wykA01 A:114-178 Trypsin-like serine proteases                  1wykA02 A:179-264 Trypsin-like serine proteases                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeeeeee..eeeee.....eee...hhh...eeehhh.eeeee..hhh.............eeeee..eeeeee..eeeee...........eee.....eeeeeeeeeee..eeeeeee.......eeee....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ALPHAVIRUS_CP  PDB: A:114-264 UniProt: 114-264                                                                                                          PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wyk A 113 MRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW 264
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with POLS_SINDO | P27285 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:152
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  
           POLS_SINDO   113 DRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW 264
               SCOP domains d1wykb_ B: Viral capsid protein                                                                                                                          SCOP domains
               CATH domains -1wykB01 B:114-178 Trypsin-like serine proteases                  1wykB02 B:179-264 Trypsin-like serine proteases                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeeeeee..eeeee.....eee...hhh...eee....eeeee..hhh.............eeeee..eeeeee..eeeee...........eee.....eeeeeeeeeee..eeeeeee.......eeee....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ALPHAVIRUS_CP  PDB: B:114-264 UniProt: 114-264                                                                                                          PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wyk B 113 MRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW 264
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with POLS_SINDO | P27285 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:152
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  
           POLS_SINDO   113 DRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW 264
               SCOP domains d1wykc_ C: Viral capsid protein                                                                                                                          SCOP domains
               CATH domains -1wykC01 C:114-178 Trypsin-like serine proteases                  1wykC02 C:179-264 Trypsin-like serine proteases                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeeeeee..eeeee.....eee...hhh...eee....eeeee..hhh.............eeeee..eeeeee..eeeee...........eee.....eeeeeeeeeee..eeeeeee.......eeee....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ALPHAVIRUS_CP  PDB: C:114-264 UniProt: 114-264                                                                                                          PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wyk C 113 MRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW 264
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with POLS_SINDO | P27285 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:152
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  
           POLS_SINDO   113 DRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW 264
               SCOP domains d1wykd_ D: Viral capsid protein                                                                                                                          SCOP domains
               CATH domains -1wykD01 D:114-178 Trypsin-like serine proteases                  1wykD02 D:179-264 Trypsin-like serine proteases                                        CATH domains
           Pfam domains (1) -Peptidase_S3-1wykD01 D:114-264                                                                                                                          Pfam domains (1)
           Pfam domains (2) -Peptidase_S3-1wykD02 D:114-264                                                                                                                          Pfam domains (2)
           Pfam domains (3) -Peptidase_S3-1wykD03 D:114-264                                                                                                                          Pfam domains (3)
           Pfam domains (4) -Peptidase_S3-1wykD04 D:114-264                                                                                                                          Pfam domains (4)
         Sec.struct. author ..eeeee.....eeeeeeee..eeeee.....eee...hhh...eeehhh.eeeee..hhhhh...........eeeee..eeeeee..eeeee...........eee.....eeeeeeeeeee..eeeeeee.......eeee....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ALPHAVIRUS_CP  PDB: D:114-264 UniProt: 114-264                                                                                                          PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wyk D 113 MRLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW 264
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (POLS_SINDO | P27285)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0039619    T=4 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=4 symmetry. The T=4 capsid is composed of 12 pentameric and 30 hexameric capsomeres.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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