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(-) Description

Title :  FITTED STRUCTURE OF ADPR-EEF2 IN THE 80S:ADPR-EEF2:GDPNP CRYO-EM RECONSTRUCTION
 
Authors :  D. J. Taylor, J. Nilsson, A. R. Merrill, G. R. Andersen, P. Nissen, J. Frank
Date :  23 Mar 07  (Deposition) - 08 May 07  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  9.70
Chains :  Asym./Biol. Unit :  S,T
Keywords :  Elongation, Translocation, Gtpase, 80S Ribosome, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Taylor, J. Nilsson, A. R. Merrill, G. R. Andersen, P. Nissen, J. Frank
Structures Of Modified Eef2. 80S Ribosome Complexes Reveal The Role Of Gtp Hydrolysis In Translocation.
Embo J. V. 26 2421 2007
PubMed-ID: 17446867  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601677
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ELONGATION FACTOR 2
    ChainsT
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymEF-2, TRANSLATION ELONGATION FACTOR 2, EUKARYOTIC ELONGATION FACTOR 2, EEF2, RIBOSOMAL TRANSLOCASE
 
Molecule 2 - ELONGATION FACTOR TU-B
    ChainsS
    FragmentSWITCH 1 LOOP
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid274
    SynonymEF-TU-B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit ST

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1APR1Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
2DDE1Mod. Amino Acid{3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H-IMIDAZOL-2-YL]-1-CARBAMOYL-PROPYL}-TRIMETHYL-AMMONIUM
3GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS T:694 , ASP T:696 , ILE T:698 , DDE T:699BINDING SITE FOR RESIDUE APR T 1699
2AC2SOFTWARETYR S:47 , ILE S:61 , THR S:62 , HIS T:27 , VAL T:28 , ASP T:29 , HIS T:30 , GLY T:31 , LYS T:32 , SER T:33 , THR T:34 , LYS T:159 , ASP T:161 , SER T:213 , GLY T:214 , LEU T:215 , HIS T:216BINDING SITE FOR RESIDUE GNP T 843

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P8X)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly T:637 -Pro T:638

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P8X)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFTU2_THET852-67  1S:51-66
EF2_YEAST58-73  1T:67-73

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2YOR133W2YOR133W.1XV:575099-5776272529EF2_YEAST1-8428421T:3-842 (gaps)840

(-) 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 S from PDB  Type:PROTEIN  Length:35
 aligned with EFTU2_THET8 | P60339 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:35
                                    45        55        65     
          EFTU2_THET8    36 TAAENPNVEVKDYGDIDKAPEERARGITINTAHVE  70
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains GTP_EFTU-2p8xS01 S:35-69            Pfam domains
         Sec.struct. author ...........hhhhh..hhhhhhhh......eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------G_TR_1          --- PROSITE
                 Transcript ----------------------------------- Transcript
                 2p8x S  35 TAAENPNVEVKDYGDIDKAPEERARGITINTAHVE  69
                                    44        54        64     

Chain T from PDB  Type:PROTEIN  Length:814
 aligned with EF2_YEAST | P32324 from UniProtKB/Swiss-Prot  Length:842

    Alignment length:840
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842
            EF2_YEAST     3 AFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTRKDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL 842
               SCOP domains d2p8xt2 T:3-343 Elongation factor 2 (eEF-2), N                  -terminal (G) domain                                                                                                                                                                                                                                                                 d2p8xt1 T:344-481 Elongation factor 2 (eEF-2), domain II                                                                                  d2p8xt4 T:482-560 Elongation factor 2 (eEF-2)                                  d2p8xt3 T:561-724 Elongation factor 2 (eEF-2), domain IV                                                                                                                 d2p8xt5 T:730-842 Elongation f   actor 2 (eEF-2)                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------GTP_EFTU-2p8xT02 T:17-344                                                                                                                                                                                                                                                                                                               ------------------------------------------------GTP_EFTU_D2-2p8xT04 T:393-470                                                 -------------------------------------------------------------------------------------------------------------------------------------EFG_IV-2p8xT03 T:604-721                                                                                              -EF     G_C-2p8xT01 T:723-811                                                             ------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhh....------------------......eeeeeeee.hhhhhhhh.......eeeeeee........hhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhh...eeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.eeeee....eeehhhhhhhhhhhhhh.hhhhhhhhh....eee....eee............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhh.......eeeeeeeee......eeeeeeeee.eee...eeeee...........eeeee..eeeeee..eeeee.eee...eeeee.........eeee..................eeeeeee.hhhhhhhhhhhhhhhhhhh...eeee.....eeeee.hhhhhhhhhhhhhhh.....eeee......eeee.......eeee......eeeeeeee.hhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhheeee.......eeeee......hhhhhhhhhhhhhhhhhhh......ee..eeeeeeeee........hhhhhhhhhhhhhhhhhhh..ee.-----.eeeeehhhhhhhhhhhhhhh..eeeeee.---...eeeeee.hhhhh.hhhhhhhhhh........................hhhhhhhhhhhhhh.......hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: T:3-842 (gaps) UniProt: 1-842 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Transcript 1
                 2p8x T   3 AFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISA------------------GITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIhRGGGQIIPTMRRATYAGFLLADPKI-----LVEIQCPEQAVGGIYSVLNKKRGQVVSEEQ---TPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL 842
                                    12        22        32        42     |   -         -    |   72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692      |702       712       722 |     732       742       752      |  -|      772       782       792       802       812       822       832       842
                                                                        48                 67                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     699-DDE                  724   730                          759 763                                                                               

   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  (4, 5)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P8X)

(-) Pfam Domains  (5, 5)

Asymmetric/Biological Unit
(-)
Clan: EF-G_C (20)
(-)
Clan: S5 (103)

(-) Gene Ontology  (16, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain S   (EFTU2_THET8 | P60339)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Chain T   (EF2_YEAST | P32324)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:1990145    maintenance of translational fidelity    Suppression of the occurrence of translational errors, such as codon-anticodon mis-paring, during the process of translation of a protein using an mRNA template.
    GO:0017183    peptidyl-diphthamide biosynthetic process from peptidyl-histidine    The modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor EF-2. The process occurs in eukaryotes and archaea but not eubacteria.
    GO:0045901    positive regulation of translational elongation    Any process that activates or increases the frequency, rate or extent of translational elongation.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    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:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EF2_YEAST | P323241n0u 1n0v 1u2r 1zm2 1zm3 1zm4 1zm9 2e1r 2npf 2p8w 2p8y 2p8z 2zit 3b78 3b82 3b8h 3dny 4v4b 5juo 5jup 5jus 5jut 5juu
        EFTU2_THET8 | P603391ha3 2c77 2p8w 2p8z 3dwu 4v5l 4v68

(-) Related Entries Specified in the PDB File

1k5x THE FITTED MODEL FOR THE 40S SUBUNIT OF THE 80S RIBOSOME
1k5y THE FITTED MODEL FOR THE 60S SUBUNIT OF THE 80S RIBOSOME
2p8w
2p8y
2p8z RELATED ID: EMD-1343 RELATED DB: EMDB