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(-) Description

Title :  STRUCTURAL BASIS OF CYTOSOLIC DNA RECOGNITION BY INNATE IMMUNE RECEPTORS
 
Authors :  T. C. Jin, T. Xiao
Date :  21 Apr 11  (Deposition) - 25 Apr 12  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,K,L,M,N
Biol. Unit 1:  A,B,K,L  (1x)
Biol. Unit 2:  C,D,M,N  (1x)
Keywords :  Ob Fold, Dna Binding, Cytosolic, Immune System-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Jin, A. Perry, J. Jiang, P. Smith, J. A. Curry, L. Unterholzner, Z. Jiang, G. Horvath, V. A. Rathinam, R. W. Johnstone, V. Hornung, E. Latz, A. G. Bowie, K. A. Fitzgerald, T. S. Xiao
Structures Of The Hin Domain:Dna Complexes Reveal Ligand Binding And Activation Mechanisms Of The Aim2 Inflammasome And Ifi16 Receptor.
Immunity V. 36 561 2012
PubMed-ID: 22483801  |  Reference-DOI: 10.1016/J.IMMUNI.2012.02.014

(-) Compounds

Molecule 1 - INTERFERON-INDUCIBLE PROTEIN AIM2
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 144-343
    GeneAIM2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymABSENT IN MELANOMA 2
 
Molecule 2 - DNA (5'- D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
    ChainsK, M
    EngineeredYES
    Other DetailsDNA 19MER
    SyntheticYES
 
Molecule 3 - DNA (5'- D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
    ChainsL, N
    EngineeredYES
    Other DetailsDNA 19MER
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDKLMN
Biological Unit 1 (1x)AB  KL  
Biological Unit 2 (1x)  CD  MN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:191 , ILE A:263 , THR A:316 , HIS A:331BINDING SITE FOR RESIDUE EDO A 2
2AC2SOFTWARELYS A:160 , ALA A:179 , THR A:180 , ASN A:265 , THR A:313BINDING SITE FOR RESIDUE EDO A 7
3AC3SOFTWARELYS B:335BINDING SITE FOR RESIDUE EDO B 5
4AC4SOFTWARELYS B:160 , ALA B:179 , THR B:180 , ASN B:265 , THR B:313BINDING SITE FOR RESIDUE EDO B 8
5AC5SOFTWARELYS C:191 , PHE C:314 , HIS C:331 , SER C:332BINDING SITE FOR RESIDUE EDO C 1
6AC6SOFTWARELYS D:191 , ILE D:263 , PHE D:314 , THR D:316 , GLY D:329 , SER D:332BINDING SITE FOR RESIDUE EDO D 3
7AC7SOFTWAREPHE D:187 , PHE D:188 , PHE D:189 , ARG D:214 , GLY D:217BINDING SITE FOR RESIDUE EDO D 4
8AC8SOFTWAREHOH D:30 , GLY D:217 , THR D:262 , ILE D:263BINDING SITE FOR RESIDUE EDO D 6
9AC9SOFTWAREHOH D:123 , THR D:180 , THR D:313BINDING SITE FOR RESIDUE EDO D 9

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RN5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RN5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

Asymmetric Unit (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043379C304YAIM2_HUMANPolymorphism778047649A/B/C/DC304Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043379C304YAIM2_HUMANPolymorphism778047649A/BC304Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043379C304YAIM2_HUMANPolymorphism778047649C/DC304Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RN5)

(-) Exons   (0, 0)

(no "Exon" information available for 3RN5)

(-) 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:194
 aligned with AIM2_HUMAN | O14862 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:194
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    
           AIM2_HUMAN   147 EGFQKRCLPVMVLKAKKPFTFETQEGKQEMFHATVATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAK 340
               SCOP domains d3rn5a1 A:147-249 automated matches                                                                    d3rn5a2 A:250-340 automated matches                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee...eeeee..eeeeeeeeeee....eeeeee.hhhhhhh.....eeeee..ee....eee....eeee.........hhhhhhhhhh..hhhhhhh.....eeeeeeeeeeeee...eeeeeeee..eeeeeeee..hhhhh.....eeeeeeeeeee....eeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------Y------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rn5 A 147 EGFQKRCLPVMVLKAKKPFTFETQEGKQEMFHATVATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAK 340
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    

Chain B from PDB  Type:PROTEIN  Length:194
 aligned with AIM2_HUMAN | O14862 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:194
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    
           AIM2_HUMAN   147 EGFQKRCLPVMVLKAKKPFTFETQEGKQEMFHATVATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAK 340
               SCOP domains d3rn5b1 B:147-249 automated matches                                                                    d3rn5b2 B:250-340 automated matches                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee...eeee....eeeeeeeeee....eeeeee.hhhhhhh.....eeeee.......eeee....eeee.........hhhhhhhhhh..hhhhhhh.....eeeeeeeeeeeee...eeeeeeee..eeeeeeee..hhhhh.....eeeeeeeeeee.....eee.....eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------Y------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rn5 B 147 EGFQKRCLPVMVLKAKKPFTFETQEGKQEMFHATVATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAK 340
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    

Chain C from PDB  Type:PROTEIN  Length:194
 aligned with AIM2_HUMAN | O14862 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:194
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    
           AIM2_HUMAN   147 EGFQKRCLPVMVLKAKKPFTFETQEGKQEMFHATVATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAK 340
               SCOP domains d3rn5c1 C:147-249 automated matches                                                                    d3rn5c2 C:250-340 automated matches                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee...eee......eeeeeeeee....eeeeee...hhhhhh....eeeeeee.....eeee....eeee.........hhhhhhhhhh..hhhhhh......eeeeeeeeeeeee...eeeeeeee..eeeeeeee...hhhhh....eeeeeeeee.......eee.....eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------Y------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rn5 C 147 EGFQKRCLPVMVLKAKKPFTFETQEGKQEMFHATVATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAK 340
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    

Chain D from PDB  Type:PROTEIN  Length:193
 aligned with AIM2_HUMAN | O14862 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:193
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337   
           AIM2_HUMAN   148 GFQKRCLPVMVLKAKKPFTFETQEGKQEMFHATVATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAK 340
               SCOP domains d3rn5d1 D:148-249 automated matches                                                                   d3rn5d2 D:250-340 automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee...eeee....eeeeeeeeee....eeeeee...hhhhhh....eeeee..ee....eee....eeee.........hhhhhhhhhh..hhhhhh.....eeeeeeeeeeeeee...eeeeeeee..eeeeeeee...hhhhh....eeeeeeeeeee....eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------Y------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rn5 D 148 GFQKRCLPVMVLKAKKPFTFETQEGKQEMFHATVATEKEFFFVKVFNTLLKDKFIPKRIIIIARYYRHSGFLEVNSASRVLDAESDQKVNVPLNIIRKAGETPKINTLQTQPLGTIVNGLFVVQKVTEKKKNILFDLSDNTGKMEVLGVRNEDTMKCKEGDKVRLTFFTLSKNGEKLQLTSGVHSTIKVIKAK 340
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337   

Chain K from PDB  Type:DNA  Length:19
                                                   
                 3rn5 K   1 CCATCAAAGAGAGAAAGAG  19
                                    10         

Chain L from PDB  Type:DNA  Length:19
                                                   
                 3rn5 L   1 GCTCTTTCTCTCTTTGATG  19
                                    10         

Chain M from PDB  Type:DNA  Length:19
                                                   
                 3rn5 M   1 CCATCAAAGAGAGAAAGAG  19
                                    10         

Chain N from PDB  Type:DNA  Length:19
                                                   
                 3rn5 N   1 GCTCTTTCTCTCTTTGATG  19
                                    10         

   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, 8)

Asymmetric Unit
(-)
Fold: OB-fold (1179)
1ad3rn5a1A:147-249
1bd3rn5d1D:148-249
1cd3rn5d2D:250-340
1dd3rn5a2A:250-340
1ed3rn5b1B:147-249
1fd3rn5b2B:250-340
1gd3rn5c1C:147-249
1hd3rn5c2C:250-340

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RN5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RN5)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (AIM2_HUMAN | O14862)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0002218    activation of innate immune response    Any process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0035458    cellular response to interferon-beta    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-beta stimulus. Interferon-beta is a type I interferon.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0050702    interleukin-1 beta secretion    The regulated release of interleukin 1 beta from a cell.
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:2001056    positive regulation of cysteine-type endopeptidase activity    Any process that activates or increases the frequency, rate or extent of cysteine-type endopeptidase activity.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0032731    positive regulation of interleukin-1 beta production    Any process that activates or increases the frequency, rate, or extent of interleukin-1 beta production.
    GO:0050718    positive regulation of interleukin-1 beta secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
    GO:0032461    positive regulation of protein oligomerization    Any process that activates or increases the frequency, rate or extent of protein oligomerization.
    GO:0070269    pyroptosis    A caspase-1-dependent cell death subroutine that is associated with the generation of pyrogenic mediators such as IL-1beta and IL-18.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0097169    AIM2 inflammasome complex    A protein complex that consists of AIM2, ASC, and caspase-1. AIM2 is a member of the HN-200 protein family that appears to be the sensor of cytosolic double-stranded DNA.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AIM2_HUMAN | O148623rn2 3vd8 4o7q

(-) Related Entries Specified in the PDB File

3rln 3rlo 3rn2 3rnu