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(-) Description

Title :  STRUCTURE OF SLYD FROM THERMUS THERMOPHILUS IN COMPLEX WITH T1 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 :  1.40
Chains :  Asym./Biol. Unit :  A,B,C
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 T1 Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD
    Chains: A
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TTHA0346
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: TTSLYD
 
Molecule 2 - GUANYL-SPECIFIC RIBONUCLEASE T1
    Chains: B, C
    Engineered: YES
    Fragment: T1 PEPTIDE (UNP RESIDUES 59-73)
    Organism Common: YELLOW KOJI MOLD
    Organism Scientific: ASPERGILLUS ORYZAE
    Organism Taxid: 5062
    Synonym: RNASE T1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:29 , LEU A:30 , ASN A:35 , HIS A:147 , ALA A:148 , HOH C:101BINDING SITE FOR RESIDUE CL A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr C:64 -Pro C:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ODK)

(-) 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:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee......hhhhhhhhh......eeeeeehhhhh....hhh.eeeee.hhh..........eeee....eeeeeeeee..eeeee.........eeeeeeeeeeee.hhhhhhhh.......eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4odk A   1 MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDNPMPLTVVAVEGEEVTVDFNHPLAGKDLDFQVEVVKVREATPEELLHGHAHPSGHHHH 156
                                    10        20        30        40        50        60        70        80        90    || 103       113       123       133       143       153   
                                                                                                                         95|                                                         
                                                                                                                          99                                                         


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               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
                 4odk B  66 HKYNNYEGx  74
                                    |
                                   74-NH2


Chain C from PDB  Type:PROTEIN  Length:3
                                   
               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
                 4odk C  64 YPH  66
   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 4ODK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

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
        RNT1_ASPOR | P00651: 1b2m 1bir 1bu4 1bvi 1ch0 1det 1fys 1fzu 1g02 1gsp 1hyf 1hz1 1i0v 1i0x 1i2e 1i2f 1i2g 1i3f 1i3i 1iyy 1lov 1low 1loy 1lra 1q9e 1rga 1rgc 1rgk 1rgl 1rhl 1rls 1rn1 1rn4 1rnt 1trp 1trq 1tto 1ygw 2aad 2aae 2bir 2bu4 2gsp 2hoh 2rnt 3bir 3bu4 3gsp 3hoh 3rnt 3syu 3urp 4bir 4bu4 4gsp 4hoh 4rnt 5bir 5bu4 5gsp 5hoh 5rnt 6gsp 6rnt 7gsp 7rnt 8rnt 9rnt
UniProtKB/TrEMBL
        Q5SLE7_THET8 | Q5SLE7: 3cgm 3cgn 3luo 4odl 4odm 4odn 4odo 4odp 4odq 4odr

(-) Related Entries Specified in the PDB File

4odl 4odm 4odn 4odo 4odp 4odq 4odr