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(-) Description

Title :  CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA (PKSI) BOUND TO 19-NORTESTOSTERONE
 
Authors :  Y. Wu, S. G. Boxer
Date :  01 Jul 16  (Deposition) - 07 Sep 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wu, S. G. Boxer
A Critical Test Of The Electrostatic Contribution To Catalysis With Noncanonical Amino Acids In Ketosteroid Isomerase.
J. Am. Chem. Soc. V. 138 11890 2016
PubMed-ID: 27545569  |  Reference-DOI: 10.1021/JACS.6B06843

(-) Compounds

Molecule 1 - STEROID DELTA-ISOMERASE
    Chains: A, B
    EC Number: 5.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: KSI
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: DELTA(5)-3-KETOSTEROID ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
16VW1Ligand/Ion(8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-METHYL-17-OXIDANYL-2,6,7,8,9,10,11,12,14,15,16,17-DODECAHYDRO-1~{H}-CYCLOPENTA[A]PHENANTHREN-3-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:93 , TYR B:16 , ASP B:40 , LEU B:99 , ASP B:103 , TRP B:120binding site for residue 6VW B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KP4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:40 -Pro A:41
2Asp B:40 -Pro B:41
3Gly B:63 -Gly B:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KP4)

(-) Exons   (0, 0)

(no "Exon" information available for 5KP4)

(-) 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:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhh.....eeee....ee....eeeeeeeeeee....eeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kp4 A   1 MNLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhh.....eeee....ee....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kp4 B   2 NLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSVR 128
                                    11        21        31        41        51        61        71        81        91       101       111       121
   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 5KP4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KP4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KP4)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  5kp4
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  5.3.3.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        SDIS_PSEPU | P07445: 1c7h 1cqs 1dmm 1dmn 1dmq 1e3r 1e3v 1e97 1ea2 1gs3 1k41 1ogx 1oh0 1oho 1opy 1vzz 1w00 1w01 1w02 1w6y 2inx 2pzv 3cpo 3fzw 3ipt 3ows 3owu 3owy 3ox9 3oxa 3rgr 3sed 3t8n 3vgn 3vsy 4cdl 4k1u 4k1v 5ai1 5d81 5d82 5d83 5g2g 5kp1 5kp3

(-) Related Entries Specified in the PDB File

5d81 5d82 5kp1 5kp3