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(-) Description

Title :  CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA (PKSI) BOUND TO EQUILENIN; D40N, Y16(CL-Y)
 
Authors :  Y. Wu, S. G. Boxer
Date :  01 Jul 16  (Deposition) - 07 Sep 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.22
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
13CT4Mod. Amino Acid3-CHLORO-L-TYROSINE
2EQU4Ligand/IonEQUILENIN
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
13CT2Mod. Amino Acid3-CHLORO-L-TYROSINE
2EQU2Ligand/IonEQUILENIN
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
13CT2Mod. Amino Acid3-CHLORO-L-TYROSINE
2EQU2Ligand/IonEQUILENIN
3SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARE3CT A:16 , ASN A:40 , VAL A:88 , MET A:90 , LEU A:99 , ASP A:103 , MET A:116 , TRP A:120 , HOH A:315 , TRP C:92 , ASN C:93binding site for residue EQU A 201
2AC2SOFTWARETHR A:5 , ALA A:6 , HIS A:78 , HOH A:302 , HOH A:314 , HOH A:322 , HOH A:404 , HOH A:410binding site for residue SO4 A 202
3AC3SOFTWARE3CT B:16 , ASN B:40 , MET B:90 , LEU B:99 , ASP B:103 , MET B:116 , TRP B:120 , HOH B:312 , ASN D:93binding site for residue EQU B 200
4AC4SOFTWARETRP A:92 , ASN A:93 , 3CT C:16 , ASN C:40 , PHE C:86 , MET C:90 , LEU C:99 , ASP C:103 , MET C:116 , TRP C:120 , HOH C:314binding site for residue EQU C 200
5AC5SOFTWARETRP B:92 , ASN B:93 , 3CT D:16 , ASN D:40 , VAL D:88 , MET D:90 , LEU D:99 , ASP D:103 , MET D:116 , TRP D:120 , HOH D:358binding site for residue EQU D 201
6AC6SOFTWARETHR D:5 , ALA D:6 , HIS D:78 , HOH D:310 , HOH D:312 , HOH D:403 , HOH D:410binding site for residue SO4 D 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KP1)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asn A:40 -Pro A:41
2Gly A:64 -Lys A:65
3Asn B:40 -Pro B:41
4Asn C:40 -Pro C:41
5Asn D:40 -Pro D:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KP1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KP1)

(-) Exons   (0, 0)

(no "Exon" information available for 5KP1)

(-) 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:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhhh....eeee....ee....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kp1 A   3 LPTAQEVQGLMARyIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    12   |    22        32        42        52        62        72        82        92       102       112       122     
                                        16-3CT                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhhh....eeee....ee....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kp1 B   3 LPTAQEVQGLMARyIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    12   |    22        32        42        52        62        72        82        92       102       112       122     
                                        16-3CT                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhhh....eeee....ee....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kp1 C   3 LPTAQEVQGLMARyIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSVR 128
                                    12   |    22        32        42        52        62        72        82        92       102       112       122      
                                        16-3CT                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhhh....eeee....ee....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kp1 D   3 LPTAQEVQGLMARyIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    12   |    22        32        42        52        62        72        82        92       102       112       122     
                                        16-3CT
   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 5KP1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KP1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KP1)

(-) Gene Ontology  (4, 4)

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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 5kp3 5kp4

(-) Related Entries Specified in the PDB File

5d81
5d82 5D82 CONTAINS THE SAME PROTEIN WITHOUT BOUND LIGAND
5kp3
5kp4