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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL REGION OF THE SCALLOP MYOSIN ROD, MONOCLINIC (C2) FORM
 
Authors :  J. H. Brown, C. Cohen
Date :  08 Nov 07  (Deposition) - 08 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Helical Coiled Coil, Disorder, Salt Links, Contractile Protein, Actin-Binding, Atp-Binding, Calmodulin- Binding, Cytoplasm, Motor Protein, Muscle Protein, Myosin, Nucleotide-Binding, Thick Filament (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. H. Brown, Y. Yang, L. Reshetnikova, S. Gourinath, D. Suveges, J. Kardos, F. Hobor, R. Reutzel, L. Nyitray, C. Cohen
An Unstable Head-Rod Junction May Promote Folding Into The Compact Off-State Conformation Of Regulated Myosins.
J. Mol. Biol. V. 375 1434 2008
PubMed-ID: 18155233  |  Reference-DOI: 10.1016/J.JMB.2007.11.071
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYOSIN HEAVY CHAIN, STRIATED MUSCLE/GENERAL CONTROL PROTEIN GCN4 CHIMERA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentBAY SCALLOP MYOSIN (RESIDUES 835-885)/YEAST GCN4 TRANSCRIPTION FACTOR (RESIDUES 250-281)
    Gene-/GCN4, AAS3, ARG9, YEL009C
    Organism Common, BAKER'S YEAST
    Organism ScientificARGOPECTEN IRRADIANS, SACCHAROMYCES CEREVISIAE
    Organism Taxid31199,4932
    Strain,
    Synonym-/AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN
    TissueADDUCTOR MUSCLE/-

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1IOD1Ligand/IonIODIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:837BINDING SITE FOR RESIDUE IOD B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BZIPPS50217 Basic-leucine zipper (bZIP) domain profile.GCN4_YEAST231-276
 
  2A:888-914
B:888-914

(-) Exons   (0, 0)

(no "Exon" information available for 3BAS)

(-) Sequences/Alignments

Asymmetric/Biological 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:80
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:171
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280 
           GCN4_YEAST   111 ENLEDNSKEWTSLFDNDIPVTTDDVSLADKAIESTEEVSLVPSNLEVSTTSFLPTPVLEDAKLTQTRKVKKPNSVVKKSHHVGKDDESRLDHLGVVAYNRKQRSIPLSPIVPESSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains d3basa_               A: Myosin S2                            N51                                                                                                           SCOP domains
               CATH domains 3basA00               A:840-919  [                            code=1.20                 .5.340, no na             me                    defined]                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh--------------hhhhhhhhhhhh----------------------------hhhhhhhhh-----------------hhhhhhhhhhhhh-------------hh-------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------BZIP  PDB: A:888-914 UniProt: 231-276         ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bas A 840 ARQEEEMK--------------EQLKQMDKMKED----------------------------LAKTERIKK-----------------ELEEQNVTLLEQK-------------ND-------------------LFGSMKQLEDKVEELLSKNYHLENEVARLKKLVGER 919
                                   | -         -  |    855   |     -         -         -  |    867|        -       870       880|        -    ||   -         -     | 888       898       908       918 
                                 847            848        859                          860     868               869         881           882|                 884                                   
                                                                                                                                             883                                                       

Chain A from PDB  Type:PROTEIN  Length:80
 aligned with MYS_ARGIR | P24733 from UniProtKB/Swiss-Prot  Length:1938

    Alignment length:115
                                   849       859       869       879       889       899       909       919       929       939       949     
            MYS_ARGIR   840 ARQEEEMKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFLQLQTLEDSMGDQEERVEKLIMQKADFESQIKELEERLLDEEDAAADLEGIKKKMEADNANLKKDIGDL 954
               SCOP domains d3basa_ A: Myosin S2N51                                                                                             SCOP domains
               CATH domains 3basA00 A:840-919  [code=1.20.5.340, no name defined]                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhh----------------------------hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3bas A 840 ARQEEEMKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFGSMKQLED-------KVEELLSKNYHLENEV----------------------------ARLKKLVGER 919
                                   849       859       869       879       889   |     - |     902      |  -         -         -     | 914     
                                                                               893     894            909                          910         

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:178
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272        
           GCN4_YEAST   103 DSTPMFEYENLEDNSKEWTSLFDNDIPVTTDDVSLADKAIESTEEVSLVPSNLEVSTTSFLPTPVLEDAKLTQTRKVKKPNSVVKKSHHVGKDDESRLDHLGVVAYNRKQRSIPLSPIVPESSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGE 280
               SCOP domains d3basb_ B: Myosi              n S2N51                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh--------------hhhhhhhhhhhh----------------------------hhhhhhhhh-----------------hhhhhhhhhhhhh-------------hh-------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------BZIP  PDB: B:888-914 UniProt: 231-276         ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bas B 832 SHMPLLSIARQEEEMK--------------EQLKQMDKMKED----------------------------LAKTERIKK-----------------ELEEQNVTLLEQK-------------ND-------------------LFGSMKQLEDKVEELLSKNYHLENEVARLKKLVGE 918
                                   841     |   -         -|      857 |       -         -         -|       |-         -      |872        |-         -  ||     -         -   |   890       900       910        
                                         847            848        859                          860     868               869         881           882|                 884                                  
                                                                                                                                                     883                                                      

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with MYS_ARGIR | P24733 from UniProtKB/Swiss-Prot  Length:1938

    Alignment length:167
                                   796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       
            MYS_ARGIR   787 AHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKWLVLRNWQWWKLYSKVKPLLSIARQEEEMKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFLQLQTLEDSMGDQEERVEKLIMQKADFESQIKELEERLLDEEDAAADLEGIKKKMEADNANLKKDIGD 953
               SCOP domains d3b                                             asb_ B: Myosin S2N51                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...---------------------------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhh----------------------------hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bas B 832 SHM---------------------------------------------PLLSIARQEEEMKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFGSMKQLED-------KVEELLSKNYHLENEV----------------------------ARLKKLVGE 918
                              |      -         -         -         -       836       846       856       866       876       886      |  -    |  899       909         -         -       911       
                            834                                           835                                                       893     894            909                          910        

   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/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GCN4_YEAST | P03069)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0001135    transcription factor activity, RNA polymerase II transcription factor recruiting    The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.
    GO:0001084    transcription factor activity, TFIID-class binding    Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001190    transcriptional activator activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
    GO:0001191    transcriptional repressor activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0010691    negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels    Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001080    nitrogen catabolite activation of transcription from RNA polymerase II promoter    A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
    GO:0045899    positive regulation of RNA polymerase II transcriptional preinitiation complex assembly    Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
    GO:1903833    positive regulation of cellular response to amino acid starvation    Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.
    GO:0060261    positive regulation of transcription initiation from RNA polymerase II promoter    Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain A,B   (MYS_ARGIR | P24733)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0003774    motor activity    Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030016    myofibril    The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.
    GO:0016459    myosin complex    A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.
    GO:0032982    myosin filament    A protein complex containing myosin heavy chains, plus associated light chains and other proteins, in which the myosin heavy chains are arranged into a filament.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GCN4_YEAST | P030691ce9 1dgc 1env 1fav 1fmh 1gcl 1gcm 1gk6 1gzl 1ihq 1ij0 1ij1 1ij2 1ij3 1kql 1ld4 1llm 1nkn 1piq 1rb4 1rb5 1rb6 1swi 1tmz 1unt 1unu 1unv 1unw 1unx 1uny 1unz 1uo0 1uo1 1uo2 1uo3 1uo4 1uo5 1w5g 1w5h 1w5i 1w5j 1w5k 1w5l 1ysa 1zii 1zij 1zik 1zil 1zim 1zta 2ahp 2b1f 2b22 2bni 2cce 2ccf 2ccn 2d3e 2dgc 2efr 2efs 2g9j 2hy6 2ipz 2k8x 2lpb 2n9b 2nrn 2o7h 2ovn 2vky 2vnl 2wg5 2wg6 2wpy 2wpz 2wq0 2wq1 2wq2 2wq3 2yny 2ynz 2yo0 2yo1 2yo2 2yo3 2z5h 2z5i 2zta 3azd 3bat 3ck4 3crp 3g9r 3gjp 3i1g 3i5c 3k7z 3m48 3p8m 3zmf 4c46 4dmd 4g2k 4hu5 4hu6 4niz 4nj0 4nj1 4nj2 4owi 4tl1 5app 5apq 5aps 5apt 5apu 5apv 5apw 5apx 5apy 5apz 5iew 5iir 5iiv 5kht
        MYS_ARGIR | P247331b7t 1dfk 1dfl 1kk7 1kk8 1kqm 1kwo 1l2o 1qvi 1s5g 1scm 1sr6 1wdc 2w4t 2w4v 2w4w 3bat 3jtd 3jvt

(-) Related Entries Specified in the PDB File

1nkn THE SAME PEPTIDE CRYSTALLIZED AT 16 DEGREES C IN THE P212121 SPACE GROUP
3bat CRYSTAL STRUCTURE OF THE N-TERMINAL REGION OF THE SCALLOP MYOSIN ROD, MONOCLINIC (P21) FORM