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(-) Description

Title :  STRUCTURE OF SLYD DELTA-IF FROM THERMUS THERMOPHILUS IN COMPLEX WITH S3 PEPTIDE
 
Authors :  E. M. Quistgaard, C. Low, P. Nordlund
Date :  10 Jan 14  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fkbp Domain, Chaperone, Peptidyl-Prolyl Isomerase, Ppiase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. M. Quistgaard, C. Low, P. Nordlund
Structure Of Slyd Delta-If From Thermus Thermophilus In Complex With S3 Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD, PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP1A CHIMERA
    ChainsA
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSEE REMARK 999
    GeneTTHA0346, FKBP1, FKBP12, FKBP1A
    Organism CommonBACTERIA, HUMAN
    Organism ScientificTHERMUS THERMOPHILUS, HOMO SAPIENS
    Organism Taxid274, 9606
    SynonymTTSLYD, PPIASE FKBP1A, 12 KDA FK506-BINDING PROTEIN, 12 KDA FKBP, FKBP-12, CALSTABIN-1, FK506-BINDING PROTEIN 1A, FKBP-1A, IMMUNOPHILIN FKBP12, ROTAMASE
 
Molecule 2 - 30S RIBOSOMAL PROTEIN S3
    ChainsB
    EngineeredYES
    FragmentS3 PEPTIDE (UNP RESIDUES 11-25)
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3NI1Ligand/IonNICKEL (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:29 , LEU A:30 , ASN A:35 , HIS A:99 , ALA A:100 , LYS B:16BINDING SITE FOR RESIDUE CL A 201
2AC2SOFTWAREHIS A:33 , ASN A:35 , HOH A:305 , HOH A:314 , HOH A:336 , HOH A:356 , HOH A:362BINDING SITE FOR RESIDUE CA A 202
3AC3SOFTWAREGLU A:49 , HOH A:313 , HOH A:326 , HOH A:382BINDING SITE FOR RESIDUE CA A 203
4AC4SOFTWAREALA A:52 , GLU A:89 , HOH A:347 , HOH A:352 , HOH A:368 , HOH A:370BINDING SITE FOR RESIDUE CA A 204
5AC5SOFTWAREGLN A:16 , HOH A:322 , HOH A:328 , HOH A:329 , HOH A:331BINDING SITE FOR RESIDUE CA A 205
6AC6SOFTWAREHIS A:97 , HIS A:99 , HIS A:101 , HIS A:106 , HIS A:108 , HIS A:110BINDING SITE FOR RESIDUE NI A 206

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ODQ)

(-) 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:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee......hhhhhhhhh......eeeeeehhhhh...........eeeeeeeeeeee.hhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4odq A   1 MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGATGHPPHATLDFQVEVVKVREATPEELLHGHAHPSGHHHHHH 110
                                    10        20        30        40        50        60       |74        84        94       104      
                                                                                              68|                                     
                                                                                               73                                     

Chain B from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4odq B  13 GIVKPW  18

   Legend:   → Mismatch (orange background)
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  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 4ODQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (55, 60)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        FKB1A_HUMAN | P629421a7x 1b6c 1bkf 1bl4 1d6o 1d7h 1d7i 1d7j 1eym 1f40 1fap 1fkb 1fkd 1fkf 1fkg 1fkh 1fki 1fkj 1fkr 1fks 1fkt 1j4h 1j4i 1j4r 1nsg 1qpf 1qpl 1tco 2dg3 2dg4 2dg9 2fap 2fke 2nd5 2ppn 2ppo 2ppp 2rse 3fap 3h9r 3mdy 4dh0 4fap 4ipx 4n19 4odp 4odr 5i7p 5i7q
        RS3_ECOLI | P0A7V31m5g 2ykr 3j9y 3j9z 3ja1 3jbu 3jbv 3jcd 3jce 3jcj 3jcn 4a2i 4adv 4u1u 4u1v 4u20 4u24 4u25 4u26 4u27 4v47 4v48 4v4h 4v4q 4v4v 4v4w 4v50 4v52 4v53 4v54 4v55 4v56 4v57 4v5b 4v5h 4v5y 4v64 4v65 4v66 4v69 4v6c 4v6d 4v6e 4v6k 4v6l 4v6m 4v6n 4v6o 4v6p 4v6q 4v6r 4v6s 4v6t 4v6v 4v6y 4v6z 4v70 4v71 4v72 4v73 4v74 4v75 4v76 4v77 4v78 4v79 4v7a 4v7b 4v7c 4v7d 4v7i 4v7s 4v7t 4v7u 4v7v 4v85 4v89 4v9c 4v9d 4v9o 4v9p 4wf1 4woi 4www 4ybb 5afi 5h5u 5iqr 5it8 5j5b 5j7l 5j88 5j8a 5j91 5jc9 5jte 5ju8 5kcr 5kcs 5kps 5kpv 5kpw 5kpx 5l3p 5lza 5lzb 5lzc 5lzd 5lze 5lzf 5mdv 5mdw 5mdy 5mdz 5me0 5me1 5mgp 5my1 5no4 5u4i 5u4j 5u9f 5u9g
UniProtKB/TrEMBL
        Q5SLE7_THET8 | Q5SLE73cgm 3cgn 3luo 4odk 4odl 4odm 4odn 4odo 4odp 4odr

(-) Related Entries Specified in the PDB File

4odk 4odl 4odm 4odn 4odo 4odp 4odr