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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN AND A 29-MER SRD RNA ANALOG
 
Authors :  X. Yang, T. Gerczei, L. Glover, C. C. Correll
Date :  06 Jun 01  (Deposition) - 26 Oct 01  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Ribotoxin, Highly Specific Ribonuclease, Protein-Rna Complex, Ribonuclease T1, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Yang, T. Gerczei, L. T. Glover, C. C. Correll
Crystal Structures Of Restrictocin-Inhibitor Complexes With Implications For Rna Recognition And Base Flipping.
Nat. Struct. Biol. V. 8 968 2001
PubMed-ID: 11685244  |  Reference-DOI: 10.1038/NSB1101-968

(-) Compounds

Molecule 1 - 29-MER SARCIN/RICIN DOMAIN RNA ANALOG
    ChainsC, D
    EngineeredYES
    Other DetailsTHE SEQUENCE CONTAINS 14 HIGHLY CONSERVED NUCLEOTIDES AMONG ALL LIVING SPECIES.
    SyntheticYES
 
Molecule 2 - RESTRICTOCIN
    ChainsA, B
    EC Number3.1.27.-
    Organism ScientificASPERGILLUS RESTRICTUS
    Organism Taxid5064
    SynonymRIBONUCLEASE MITOGILLIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric Unit (5, 30)
No.NameCountTypeFull Name
1A2M2Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2K6Ligand/IonPOTASSIUM ION
3OMC10Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
4OMG10Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
5OMU2Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1A2M1Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2K-1Ligand/IonPOTASSIUM ION
3OMC5Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
4OMG5Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
5OMU1Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
1A2M1Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2K-1Ligand/IonPOTASSIUM ION
3OMC5Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
4OMG5Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
5OMU1Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREOMG D:24 , HOH D:407 , HOH D:411 , HOH D:439 , HOH D:440BINDING SITE FOR RESIDUE K D 401
2AC2SOFTWAREU D:7 , HOH D:404 , HOH D:414 , HOH D:456 , HOH D:468BINDING SITE FOR RESIDUE K D 402
3AC3SOFTWAREHOH B:172 , HOH B:179 , HOH B:200 , G D:14 , HOH D:416 , HOH D:446 , HOH D:460BINDING SITE FOR RESIDUE K D 403
4AC4SOFTWAREOMG C:24 , HOH C:414 , HOH C:417 , HOH C:422 , HOH C:425BINDING SITE FOR RESIDUE K C 404
5AC5SOFTWAREU C:7 , HOH C:408 , HOH C:410 , HOH C:428 , HOH C:436 , HOH C:452BINDING SITE FOR RESIDUE K C 405
6AC6SOFTWAREHOH A:216 , G C:14 , HOH C:435 , HOH C:446BINDING SITE FOR RESIDUE K C 406

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:5 -A:147
2A:75 -A:131
3B:5 -B:147
4B:75 -B:131

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:47 -Pro A:48
2Lys A:111 -Pro A:112
3Tyr A:125 -Pro A:126
4Tyr B:47 -Pro B:48
5Lys B:111 -Pro B:112
6Tyr B:125 -Pro B:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JBS)

(-) Exons   (0, 0)

(no "Exon" information available for 1JBS)

(-) 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:149
 aligned with RNMG_ASPFU | P67875 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:149
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167         
           RNMG_ASPFU    28 ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH 176
               SCOP domains d1jbsa_ A: Restrictocin                                                                                                                               SCOP domains
               CATH domains 1jbsA00 A:1-149  [code=3.10.450.30, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....eeeeeeeeeehhhhhhhhhhh............eee....................hhhhhh..............eeeeee.....................eeeeeee....eeeeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jbs A   1 ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain A from PDB  Type:PROTEIN  Length:149
 aligned with RNMG_ASPRE | P67876 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:149
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167         
           RNMG_ASPRE    28 ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH 176
               SCOP domains d1jbsa_ A: Restrictocin                                                                                                                               SCOP domains
               CATH domains 1jbsA00 A:1-149  [code=3.10.450.30, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....eeeeeeeeeehhhhhhhhhhh............eee....................hhhhhh..............eeeeee.....................eeeeeee....eeeeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jbs A   1 ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with RNMG_ASPFU | P67875 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:149
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167         
           RNMG_ASPFU    28 ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH 176
               SCOP domains d1jbsb_ B: Restrictocin                                                                                                                               SCOP domains
               CATH domains 1jbsB00 B:1-149  [code=3.10.450.30, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee......eeeeeeeeehhhhhhhhhhh............ee.....................hhhhhh..............eeeeee.....................eeeeeee....eeeeee.........ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jbs B   1 ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with RNMG_ASPRE | P67876 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:149
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167         
           RNMG_ASPRE    28 ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH 176
               SCOP domains d1jbsb_ B: Restrictocin                                                                                                                               SCOP domains
               CATH domains 1jbsB00 B:1-149  [code=3.10.450.30, no name defined]                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee......eeeeeeeeehhhhhhhhhhh............ee.....................hhhhhh..............eeeeee.....................eeeeeee....eeeeee.........ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jbs B   1 ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         

Chain C from PDB  Type:DNA/RNA  Length:29
                                                             
                 1jbs C   1 cgcuccUCAGUACGAUAGGAACCggagcg  29
                            ||||||  10        20   ||||||
                            1-OMC|                24-OMG|
                             2-OMG                 25-OMG
                              3-OMC                 26-A2M
                               4-OMU                 27-OMG
                                5-OMC                 28-OMC
                                 6-OMC                 29-OMG

Chain D from PDB  Type:DNA/RNA  Length:29
                                                             
                 1jbs D   1 cgcuccUCAGUACGAUAGGAACCggagcg  29
                            ||||||  10        20   ||||||
                            ||||||                24-OMG|
                            1-OMC|                 25-OMG
                             2-OMG                  26-A2M
                              3-OMC                  27-OMG
                               4-OMU                  28-OMC
                                5-OMC                  29-OMG
                                 6-OMC                   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JBS)

(-) Gene Ontology  (13, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RNMG_ASPFU | P67875)
molecular function
    GO:0019863    IgE binding    Interacting selectively and non-covalently with an immunoglobulin of the IgE isotype.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0060300    regulation of cytokine activity    Any process that modulates the rate, frequency or extent of the activity of a molecule that controls the survival, growth, differentiation and effector function of tissues and cells.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A,B   (RNMG_ASPRE | P67876)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RNMG_ASPRE | P678761aqz 1jbr 1jbt

(-) Related Entries Specified in the PDB File

1aqz CRYSTAL STRUCTURE OF A HIGHLY SPECIFIC ASPERGILLUS RIBOTOXIN, RESTRICTOIN
1jbr CRYSTAL STRUCTURE OF THE RIBOTOXIN RESTRICTOCIN AND A 31- MER SRD RNA INHIBITOR
1jbt CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG
430d STRUCTURE OF SARCIN/RICIN LOOP FROM RAT 28S RNA
480d CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23S RRNA
483d CRYSTAL STRUCTURE OF THE SARIN/RICIN DOMAIN FROM E.COLI 23S RRNA