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(-) Description

Title :  RIBOSOMAL PROTEIN L1 FROM THERMUS THERMOPHILUS WITH SUBSTITUTION THR217ALA
 
Authors :  V. G. Kljashtorny, S. A. Volchkov, E. Y. Nikonova, O. S. Kostareva, S. V. Tishchenko, N. A. Nevskaya, S. V. Nikonov
Date :  21 May 12  (Deposition) - 08 Aug 12  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Ribosomal Protein, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. I. U. Nikonova, S. A. Volchkov, V. G. Kliashtornyi, S. V. Tishchenko O. S. Kostareva, N. A. Nevskaia, O. S. Nikonov, A. G. Gabdulkhakov, A. D. Nikulin, N. L. Davydova, V. A. Strel'Tsov, M. B. Garber, S. V. Nikonov
[Crystal Structures Of Mutant Ribosomal Proteins L1].
Mol. Biol. (Moscow) V. 41 688 2007
PubMed-ID: 17936990

(-) Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L1
    Chains: A
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3SO410Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:67 , VAL A:72 , ASP A:111 , GLY A:176 , LYS A:177 , MPD A:303 , HOH A:473BINDING SITE FOR RESIDUE MPD A 301
02AC2SOFTWAREARG A:8 , LEU A:11 , GLU A:12 , ILE A:193 , GLU A:197 , HIS A:227 , HOH A:653BINDING SITE FOR RESIDUE MPD A 302
03AC3SOFTWARETHR A:40 , ALA A:112 , VAL A:113 , GLY A:135 , LEU A:136 , ILE A:161 , PRO A:174 , LYS A:177 , MPD A:301 , HOH A:440 , HOH A:441 , HOH A:597 , HOH A:611BINDING SITE FOR RESIDUE MPD A 303
04AC4SOFTWARELYS A:2 , ASN A:148 , GLU A:151 , GLU A:155 , GLU A:162 , HOH A:528BINDING SITE FOR RESIDUE MRD A 304
05AC5SOFTWAREARG A:53 , LYS A:79 , GLY A:80 , ILE A:83 , GLY A:96 , HOH A:420 , HOH A:471 , HOH A:555 , HOH A:590 , HOH A:683 , HOH A:684BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREGLU A:197 , LYS A:200 , THR A:207 , PHE A:208 , LEU A:209 , HIS A:227 , HOH A:449 , HOH A:477 , HOH A:564 , HOH A:671BINDING SITE FOR RESIDUE SO4 A 306
07AC7SOFTWAREPRO A:65 , HIS A:66 , GLY A:67 , GLN A:71 , LYS A:184 , HOH A:406 , HOH A:696 , HOH A:704BINDING SITE FOR RESIDUE SO4 A 307
08AC8SOFTWARELYS A:18 , GLY A:60 , THR A:61 , HIS A:199 , HOH A:491 , HOH A:634BINDING SITE FOR RESIDUE SO4 A 308
09AC9SOFTWAREHIS A:27 , GLN A:101 , LYS A:126 , PRO A:182 , GLU A:183 , HOH A:427 , HOH A:553 , HOH A:642 , HOH A:647BINDING SITE FOR RESIDUE SO4 A 309
10BC1SOFTWARETYR A:7 , LYS A:82 , SER A:221 , HOH A:576BINDING SITE FOR RESIDUE SO4 A 310
11BC2SOFTWAREHIS A:172 , HOH A:452 , HOH A:570 , HOH A:573BINDING SITE FOR RESIDUE SO4 A 311
12BC3SOFTWARELYS A:2 , HIS A:3 , GLY A:4 , TYR A:7 , MET A:218BINDING SITE FOR RESIDUE SO4 A 312
13BC4SOFTWAREHIS A:44 , TYR A:213 , THR A:215 , SER A:221 , HOH A:516 , HOH A:680BINDING SITE FOR RESIDUE SO4 A 313
14BC5SOFTWARETHR A:34 , ALA A:35 , LYS A:36 , ARG A:73 , HOH A:588 , HOH A:674BINDING SITE FOR RESIDUE SO4 A 314

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F9T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F9T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F9T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F9T)

(-) Exons   (0, 0)

(no "Exon" information available for 4F9T)

(-) 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.......hhhhhhhhhhhhh......eeeeeeee.....hhhhh.eeee...........eeee..hhhhhhhhhh...eee..hhhhhhhh......eeee...hhhhhhhhhhhhhhhhh............hhhhhhhhhhh..eeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhh.........eeeeeee......ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9t A   1 PKHGYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTAMGPSVRINPHS 228
                               ||   12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      
                               4|                                                                                                                                                                                                                             
                                7
   Legend:   → Mismatch (orange background)
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  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 4F9T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F9T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F9T)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RL1_THETH | P27150: 1ad2 1eg0 1zho 2hw8 2oum 2ov7 2vpl 3tg8 3u4m 3u56 3umy 487d 4qg3 4qgb 4qvi 4reo 5ib7 5ib8 5ibb 5imq 5imr 5j8b

(-) Related Entries Specified in the PDB File

1ad2 L1 MUTANT WITH SERINE 179 REPLACED BY CYSTEINE
1i2a L1 FROM METHANOCOCCUS JANNASCHII
1mzp STRUCTURE OF THE L1 PROTUBERANCE IN THE RIBOSOME
1u63 L1-MRNA COMPLEX FROM METHANOCOCCUS JANNASCHII
1zho L1 IN COMPLEX WITH MRNA AT 2.6 RESOLUTION
2hw8 L1-MRNA COMPLEX AT 2.1 RESOLUTION
2oum THE FIRST DOMAIN OF L1 FROM THERMUS THERMOPHILUS
2ov7 THE FIRST DOMAIN OF L1 FROM THERMUS THERMOPHILUS
2vpl THE STRUCTURE OF THE COMPLEX BETWEEN THE FIRST DOMAIN OF L1 PROTEIN FROM THERMUS THERMOPHILUS AND MRNA FROM METHANOCOCCUS JANNASCHII