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(-) Description

Title :  IMP1 KH34
 
Authors :  J. A. Chao, R. H. Singer, S. C. Almo, Y. Patskovsky
Date :  18 Nov 09  (Deposition) - 09 Feb 10  (Release) - 23 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x)
Biol. Unit 5:  A (1x),B (1x)
Biol. Unit 6:  A,C  (1x)
Keywords :  Rna Binding Protein, Kh Domain, Cell Projection, Cytoplasm, Nucleus, Phosphoprotein, Rna-Binding, Translation Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Chao, Y. Patskovsky, V. Patel, M. Levy, S. C. Almo, R. H. Singer
Zbp1 Recognition Of Beta-Actin Zipcode Induces Rna Looping.
Genes Dev. V. 24 148 2010
PubMed-ID: 20080952  |  Reference-DOI: 10.1101/GAD.1862910

(-) Compounds

Molecule 1 - INSULIN-LIKE GROWTH FACTOR 2 MRNA-BINDING PROTEIN 1
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainROSETTA2
    Expression System Taxid562
    FragmentRESIDUES 404-566
    GeneIGF2BP1, CRDBP, VICKZ1, ZBP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIGF2 MRNA-BINDING PROTEIN 1, IMP-1, IGF-II MRNA- BINDING PROTEIN 1, CODING REGION DETERMINANT-BINDING PROTEIN, CRD-BP, VICKZ FAMILY MEMBER 1, ZIP CODE-BINDING PROTEIN 1, ZIPCODE-BINDING PROTEIN 1, ZBP-1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C
Biological Unit 4 (1x)A (1x)B (1x)C (1x)
Biological Unit 5 (1x)A (1x)B (1x) 
Biological Unit 6 (1x)A C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 6 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:544 , GLU B:406 , GLN B:547 , ARG B:551 , ARG B:554BINDING SITE FOR RESIDUE GOL B 1
2AC2SOFTWAREVAL A:451 , GLU A:489 , HIS A:491 , GLU C:445BINDING SITE FOR RESIDUE GOL A 2
3AC3SOFTWAREPHE B:411 , VAL B:451 , GLU B:489 , HIS B:491BINDING SITE FOR RESIDUE GOL B 3
4AC4SOFTWAREGLY A:468 , TYR A:471 , TYR A:544 , PHE B:464BINDING SITE FOR RESIDUE GOL A 4

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:481 -Pro A:482
2Gly C:481 -Pro C:482

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KRM)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.IF2B1_HUMAN195-260
276-343
405-470
 
 
487-553
 
 
  6-
-
A:405-470
B:405-470
C:405-470
A:487-553
B:487-553
C:487-553
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.IF2B1_HUMAN195-260
276-343
405-470
 
 
487-553
 
 
  2-
-
A:405-470
-
-
A:487-553
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.IF2B1_HUMAN195-260
276-343
405-470
 
 
487-553
 
 
  2-
-
-
B:405-470
-
-
B:487-553
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.IF2B1_HUMAN195-260
276-343
405-470
 
 
487-553
 
 
  2-
-
-
-
C:405-470
-
-
C:487-553
Biological Unit 4 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.IF2B1_HUMAN195-260
276-343
405-470
 
 
487-553
 
 
  6-
-
A:405-470
B:405-470
C:405-470
A:487-553
B:487-553
C:487-553
Biological Unit 5 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.IF2B1_HUMAN195-260
276-343
405-470
 
 
487-553
 
 
  4-
-
A:405-470
B:405-470
-
A:487-553
B:487-553
-
Biological Unit 6 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.IF2B1_HUMAN195-260
276-343
405-470
 
 
487-553
 
 
  4-
-
A:405-470
-
C:405-470
A:487-553
-
C:487-553

(-) Exons   (0, 0)

(no "Exon" information available for 3KRM)

(-) 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:158
 aligned with IF2B1_HUMAN | Q9NZI8 from UniProtKB/Swiss-Prot  Length:577

    Alignment length:158
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554        
          IF2B1_HUMAN   405 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ 562
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhh..hhhhhhhhhhhh.eeee.........eeeeeeeehhhhhhhhhhhhhhhhhhh..........eeeeeeee..hhhhhhh..hhhhhhhhhhhh.eee...........eeeeeeeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE KH_TYPE_1  PDB: A:405-470 UniProt: 405-470                        ----------------KH_TYPE_1  PDB: A:487-553 UniProt: 487-553                         --------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3krm A 405 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ 562
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554        

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with IF2B1_HUMAN | Q9NZI8 from UniProtKB/Swiss-Prot  Length:577

    Alignment length:158
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554        
          IF2B1_HUMAN   405 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ 562
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhh..hhhhhhhhhhh..eeee.........eeeeeeeehhhhhhhhhhhhhhhhhhh....--....eeeeeeee..hhhhhhh..hhhhhhhhhhhh.eee...........eeeeeeeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE KH_TYPE_1  PDB: B:405-470 UniProt: 405-470                        ----------------KH_TYPE_1  PDB: B:487-553 UniProt: 487-553                         --------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3krm B 405 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFG--EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ 562
                                   414       424       434       444       454       464       474      |484       494       504       514       524       534       544       554        
                                                                                                      481  |                                                                              
                                                                                                         484                                                                              

Chain C from PDB  Type:PROTEIN  Length:157
 aligned with IF2B1_HUMAN | Q9NZI8 from UniProtKB/Swiss-Prot  Length:577

    Alignment length:158
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554        
          IF2B1_HUMAN   405 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ 562
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------KH_1-3krmC01 C:489-553                                           --------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------KH_1-3krmC02 C:489-553                                           --------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------KH_1-3krmC03 C:489-553                                           --------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------KH_1-3krmC04 C:489-553                                           --------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------KH_1-3krmC05 C:489-553                                           --------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------KH_1-3krmC06 C:489-553                                           --------- Pfam domains (6)
         Sec.struct. author .eeeeeeee..hhhhhhh..hhhhhhhhhhhh.eeee.........eeeeeeeehhhhhhhhhhhhhhhhhhh.....-....eeeeeeee..hhhhhhh..hhhhhhhhhhhh.eee...........eeeeeeeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE KH_TYPE_1  PDB: C:405-470 UniProt: 405-470                        ----------------KH_TYPE_1  PDB: C:487-553 UniProt: 487-553                         --------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3krm C 405 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGP-EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ 562
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554        
                                                                                                       482 |                                                                              
                                                                                                         484                                                                              

   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  (0, 0)

(no "SCOP Domain" information available for 3KRM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: KH (43)
(-)
Family: KH_1 (21)
1aKH_1-3krmC01C:489-553
1bKH_1-3krmC02C:489-553
1cKH_1-3krmC03C:489-553
1dKH_1-3krmC04C:489-553
1eKH_1-3krmC05C:489-553
1fKH_1-3krmC06C:489-553

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (IF2B1_HUMAN | Q9NZI8)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    GO:0048027    mRNA 5'-UTR binding    Interacting selectively and non-covalently with the 5' untranslated region of an mRNA molecule.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
    GO:0045182    translation regulator activity    Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
biological process
    GO:0070934    CRD-mediated mRNA stabilization    An mRNA stabilization process in which one or more RNA-binding proteins associate with a sequence in the open reading frame called the coding region instability determinant (CRD).
    GO:0006403    RNA localization    A process in which RNA is transported to, or maintained in, a specific location.
    GO:0010467    gene expression    The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0097150    neuronal stem cell population maintenance    Any process in by an organism or tissue maintains a population of neuronal stem cells.
    GO:0022013    pallium cell proliferation in forebrain    The multiplication or reproduction of pallium cells in the forebrain, resulting in the expansion of the cell population.
    GO:0042035    regulation of cytokine biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cytokines.
    GO:0010610    regulation of mRNA stability involved in response to stress    Any process that modulates the propensity of mRNA molecules to degradation that is part of a change in state or activity of a cell as a result of an exogenous disturbance.
    GO:0006417    regulation of translation    Any process that modulates 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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0070937    CRD-mediated mRNA stability complex    A protein complex that binds to, and promotes stabilization of, mRNA molecules containing the coding region instability determinant (CRD). In human, it may consist of IGF2BP1, HNRNPU, SYNCRIP/HNRNPQ, YBX1, and DHX9.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    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:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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