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(-) Description

Title :  S1P LYASE BACTERIAL SURROGATE BOUND TO N-(1-(4-(3-HYDROXYPROP-1-YN-1-YL)PHENYL)-2-((4-METHOXY-2,5-DIMETHYLBENZYL)AMINO)ETHYL)-5-METHYLISOXAZOLE-3-CARBOXAMIDE
 
Authors :  M. A. Argiriadi, D. Banach, E. Radziejewska, S. Marchie, J. Dimauro, J. E. Dominguez, C. Hutchins, R. A. Judge, K. Queeney, G. Wallace, C. M. Ha
Date :  18 Nov 15  (Deposition) - 16 Mar 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B
Keywords :  S1P Lyase Bacterial Surrogate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Argiriadi, D. Banach, E. Radziejewska, S. Marchie, J. Dimauro, J. Dinges, E. Dominguez, C. Hutchins, R. A. Judge, K. Queeney, G. Wallace, C. M. Harris
Creation Of A S1P Lyase Bacterial Surrogate For Structure-Based Drug Design.
Bioorg. Med. Chem. Lett. V. 26 2293 2016
PubMed-ID: 27013389  |  Reference-DOI: 10.1016/J.BMCL.2016.02.084

(-) Compounds

Molecule 1 - PUTATIVE SPHINGOSINE-1-PHOSPHATE LYASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: STH1274
    Mutation: YES
    Organism Scientific: SYMBIOBACTERIUM THERMOPHILUM (STRAIN T / IAM 14863)
    Organism Taxid: 292459
    Strain: T / IAM 14863

 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
15S62Ligand/Ion~{N}-[(1~{S})-2-[(4-METHOXY-2,5-DIMETHYL-PHENYL)METHYLAMINO]-1-[4-(3-OXIDANYLPROP-1-YNYL)PHENYL]ETHYL]-5-METHYL-1,2-OXAZOLE-3-CARBOXAMIDE
2LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:103 , TYR A:105 , LLP A:311 , HOH A:705 , HOH A:732 , HOH A:775 , ASN B:126 , HIS B:129binding site for residue PO4 A 601
2AC2SOFTWAREHIS A:201 , PHE A:249 , LLP A:311 , VAL A:496 , PHE A:500 , PRO B:127 , LEU B:128 , PRO B:130 , TRP B:340 , GLY B:342 , ILE B:344 , TYR B:345 , ALA B:346 , HOH B:714binding site for residue 5S6 A 602
3AC3SOFTWARELEU A:128 , PRO A:130 , TRP A:340 , GLY A:342 , ILE A:344 , TYR A:345 , ALA A:346 , HOH A:712 , HOH A:747 , HIS B:201 , PHE B:249 , LLP B:311 , SER B:497 , PHE B:500binding site for residue 5S6 A 603
4AC4SOFTWAREASN A:126 , LEU A:128 , HIS A:129 , HOH A:712 , HOH A:745 , ALA B:103 , TYR B:105 , LLP B:311 , HOH B:703 , HOH B:738 , HOH B:741 , HOH B:800binding site for residue PO4 B 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:246 -Pro A:247
2Arg A:436 -Pro A:437
3Ala B:246 -Pro B:247
4Arg B:436 -Pro B:437

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EUD)

(-) 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:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee......hhhhhhhh...............eeee............eeeee.hhhhhhhhheee.......eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee......eeeee....hhhhhhhhhhhh....eee....eeeee.hhhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eud A  55 SQIKPYRDRFPSHARLPRAGLPRAEILAEIAAMGAAESPAWRDGYASGAVYHGDEHHIAFLNEVYALQSQSNPLHPDLWPSTAKFEAEVVAMTAHMLGGDAAGGTVCGTVTSGGTESLLLAMKTYRDWARATKGITAPEAVVPVSAHAAFDKAAQYFGIKLVRTPLDADYRADVAAMREAITPNTVVVAGSAPGFPHGVVDPIPEIAALAAEHGIGCHVDACLGGFILPWAERLGYPVPPFDFRLEGVTSVSADTHkYGYGAKGTSVILYRRPDLLHYQYFIAADWPGGIYASPTFAGSRPGALSATAWAAMLSLGEEGYLDATRRILQAADRLKAGVRAIPSLKILGDPLWVIAVASDELNIYQVMEEMAGRGWRLNGLHRPPAFHVALTLRHTEPGVVDRFLADLQDAVAQVRAHPEKATGMAPVYGMAAAAPPELVRQVSTGFIDLLYEVH 508
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304      |314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504    
                                                                                                                                                                                                                                                                                          311-LLP                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee......hhhhhhhh...............eeee............eeeee.hhhhhh...eee.......eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee......eeeee....hhhhhhhhhhhh....eee....eeeee.hhhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eud B  59 PYRDRFPSHARLPRAGLPRAEILAEIAAMGAAESPAWRDGYASGAVYHGDEHHIAFLNEVYALQSQSNPLHPDLWPSTAKFEAEVVAMTAHMLGGDAAGGTVCGTVTSGGTESLLLAMKTYRDWARATKGITAPEAVVPVSAHAAFDKAAQYFGIKLVRTPLDADYRADVAAMREAITPNTVVVAGSAPGFPHGVVDPIPEIAALAAEHGIGCHVDACLGGFILPWAERLGYPVPPFDFRLEGVTSVSADTHkYGYGAKGTSVILYRRPDLLHYQYFIAADWPGGIYASPTFAGSRPGALSATAWAAMLSLGEEGYLDATRRILQAADRLKAGVRAIPSLKILGDPLWVIAVASDELNIYQVMEEMAGRGWRLNGLHRPPAFHVALTLRHTEPGVVDRFLADLQDAVAQVRAHPEKATGMAPVYGMAAAAPPELVRQVSTGFIDLLYEV 507
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308  |    318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498         
                                                                                                                                                                                                                                                                                      311-LLP
   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 5EUD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        Q67PY4_SYMTH | Q67PY4: 3mad 3maf 3mau 3mbb 5eue

(-) Related Entries Specified in the PDB File

5eue