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(-) Description

Title :  STRUCTURE OF SLYD FROM THERMUS THERMOPHILUS IN COMPLEX WITH S2 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 :  2.92
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D,F  (1x)
Biol. Unit 2:  B,C,E  (1x)
Keywords :  Fkbp Domain, If 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 From Thermus Thermophilus In Complex With S2 Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD
    ChainsA, B
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneTTHA0346
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid274
    SynonymTTSLYD
 
Molecule 2 - 30S RIBOSOMAL PROTEIN S2
    ChainsC, D, E, F
    EngineeredYES
    FragmentS2 PEPTIDE (UNP RESIDUES 20-34)
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A  D F
Biological Unit 2 (1x) BC E 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NH24Mod. Amino AcidAMINO GROUP
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NH22Mod. Amino AcidAMINO GROUP
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NH22Mod. Amino AcidAMINO GROUP

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:29 , LEU A:30 , ASN A:35 , ALA A:148 , LYS F:28BINDING SITE FOR RESIDUE CL A 201
2AC2SOFTWAREASP A:82 , LEU B:30 , ASN B:35 , ALA B:148 , LYS E:28BINDING SITE FOR RESIDUE CL B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys C:28 -Pro C:29
2Thr D:20 -Arg D:21
3Lys E:28 -Pro E:29
4Lys F:28 -Pro F:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ODL)

(-) 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:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee......hhhhhhhhh......eeeeeehhhhh....hhh.eeeee.hhh..........eeeee......eeeeeeeee..eeeee.........eeeeeeeeeeee.hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4odl A   1 MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHPLAGKDLDFQVEVVKVREATPEELLHGHAHP 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee......hhhhhhhhh......eeeeeehhhhh....hhh.eeeee.hhh..........eeeee.....eeeeeeeeee..eeeee.........eeeeeeeeeeee.hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4odl B   1 MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHPLAGKDLDFQVEVVKVREATPEELLHGHAHP 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:10
                                          
               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
                 4odl C  26 KMKPFIFGAx  35
                                    35
                                    35-NH2

Chain D from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..........eee... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 4odl D  20 TRYWNPKMKPFIFGAx  35
                                    29     |
                                          35-NH2

Chain E from PDB  Type:PROTEIN  Length:16
                                                
               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
                 4odl E  20 TRYWNPKMKPFIFGAx  35
                                    29     |
                                          35-NH2

Chain F from PDB  Type:PROTEIN  Length:16
                                                
               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
                 4odl F  20 TRYWNPKMKPFIFGAx  35
                                    29     |
                                          35-NH2

   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 4ODL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RS2_ECOLI | P0A7V01m5g 2ykr 3j9y 3j9z 3ja1 3jbu 3jbv 3jcd 3jce 3jcj 3jcn 4a2i 4adv 4odm 4odn 4odp 4u1u 4u1v 4u20 4u24 4u25 4u26 4u27 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 5no3 5u4i
UniProtKB/TrEMBL
        Q5SLE7_THET8 | Q5SLE73cgm 3cgn 3luo 4odk 4odm 4odn 4odo 4odp 4odq 4odr

(-) Related Entries Specified in the PDB File

4odk 4odm 4odn 4odo 4odp 4odq 4odr