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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF HALOTAG BOUND TO THE P1 BENZOXADIAZOLE FLUOROGENIC LIGAND
 
Authors :  N. P. Dunham, A. K. Boal
Date :  01 May 17  (Deposition) - 14 Jun 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Biosensor, Cytotoxicity, Fluorescent Probe, Protein Aggregation, Proteome Stress, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, M. Fares, N. P. Dunham, Z. Gao, K. Miao, X. Jiang, S. S. Bollinger A. K. Boal, X. Zhang
Aghalo: A Facile Fluorogenic Sensor To Detect Drug Induced Proteome Stress.
Angew. Chem. Int. Ed. Engl. 2017
PubMed-ID: 28557281  |  Reference-DOI: 10.1002/ANIE.201702417

(-) Compounds

Molecule 1 - HALOALKANE DEHALOGENASE
    Chains: A, B
    EC Number: 3.8.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: DHAA
    Organism Scientific: RHODOCOCCUS RHODOCHROUS
    Organism Taxid: 1829

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
19FM2Ligand/IonN-{2-[2-(HEXYLOXY)ETHOXY]ETHYL}-N~2~-METHYL-N~2~-{[7-(METHYLAMINO)-2,1,3-BENZOXADIAZOL-4-YL]SULFONYL}GLYCINAMIDE
2CL2Ligand/IonCHLORIDE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
19FM1Ligand/IonN-{2-[2-(HEXYLOXY)ETHOXY]ETHYL}-N~2~-METHYL-N~2~-{[7-(METHYLAMINO)-2,1,3-BENZOXADIAZOL-4-YL]SULFONYL}GLYCINAMIDE
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
19FM1Ligand/IonN-{2-[2-(HEXYLOXY)ETHOXY]ETHYL}-N~2~-METHYL-N~2~-{[7-(METHYLAMINO)-2,1,3-BENZOXADIAZOL-4-YL]SULFONYL}GLYCINAMIDE
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:105 , THR A:147 , PHE A:148 , GLN A:164 , VAL A:166 , THR A:171 , MET A:174 , ASN A:271 , CL A:302binding site for residue 9FM A 301
2AC2SOFTWAREASN A:40 , TRP A:106 , PRO A:205 , 9FM A:301binding site for residue CL A 302
3AC3SOFTWAREASN B:40 , TRP B:106 , PRO B:205 , 9FM B:301binding site for residue CL B 302
4AC4SOFTWAREGLY B:39 , ASN B:40 , HIS B:104 , TRP B:106 , GLY B:107 , SER B:108 , ALA B:109 , GLU B:129 , ILE B:131 , ALA B:144 , THR B:147 , GLY B:170 , THR B:171 , MET B:174 , GLY B:175 , LEU B:245 , ASN B:271 , CL B:302binding site for Di-peptide 9FM B 301 and ASP B 105

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asn A:40 -Pro A:41
2Glu A:213 -Pro A:214
3Thr A:241 -Pro A:242
4Asn B:40 -Pro B:41
5Glu B:213 -Pro B:214
6Thr B:241 -Pro B:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VNP)

(-) 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:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee..eeeeeeee.......eeee.....hhhhhh.hhhhhh....eeee...............hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vnp A   3 IGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVAPTHRCIAPDLIGMGKSDKPDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIAFMEFIRPIPTWDEWPEFARETFQAFRTTDVGRKLIIDQNVFIEGTLPMGVVRPLTEVEMDHYREPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPVPKLLFWGTPGVLIPPAEAARLAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTL 292
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee..eeeeeeee.......eeee.....hhhhhh.hhhhhh....eeee...............hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhh.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vnp B   3 IGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVAPTHRCIAPDLIGMGKSDKPDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIAFMEFIRPIPTWDEWPEFARETFQAFRTTDVGRKLIIDQNVFIEGTLPMGVVRPLTEVEMDHYREPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPVPKLLFWGTPGVLIPPAEAARLAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTL 292
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
   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 5VNP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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  5vnp
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  DHAA_RHORH | P0A3G2
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 Related Entries

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

UniProtKB/Swiss-Prot
        DHAA_RHORH | P0A3G2: 2v9z 3fbw 3rk4 3sk0 4e46 4f5z 4f60 4fwb 4wcv 5flk 5uxz 5uy1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5VNP)