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(-) Description

Title :  DCPS IN COMPLEX WITH COVALENT LIGAND
 
Authors :  S. Liu
Date :  14 May 14  (Deposition) - 20 May 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Decapping Scavenger Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liu
Dcps In Complex With Covalent Ligands Targeting Tyrosines
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - M7GPPPX DIPHOSPHATASE
    Chains: A, B, C, D
    EC Number: 3.6.1.59
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DCPS, DCS1, HINT5, HSPC015
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DCS-1, DECAPPING SCAVENGER ENZYME, HINT-RELATED 7MEGMP- DIRECTED HYDROLASE, HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN 5, HISTIDINE TRIAD PROTEIN MEMBER 5, HINT-5, SCAVENGER MRNA-DECAPPING ENZYME DCPS

 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, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
130U2Ligand/Ion4-{[(2,4-DIAMINOQUINAZOLIN-5-YL)OXY]METHYL}BENZENESULFONIC ACID
2GOL1Ligand/IonGLYCEROL
3PO410Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
130U1Ligand/Ion4-{[(2,4-DIAMINOQUINAZOLIN-5-YL)OXY]METHYL}BENZENESULFONIC ACID
2GOL-1Ligand/IonGLYCEROL
3PO46Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
130U1Ligand/Ion4-{[(2,4-DIAMINOQUINAZOLIN-5-YL)OXY]METHYL}BENZENESULFONIC ACID
2GOL1Ligand/IonGLYCEROL
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:130 , VAL A:132 , TYR A:143 , TRP A:175 , GLU A:185 , ARG A:188 , PRO A:204 , ASP A:205 , LEU A:206 , ILE A:219 , ASN B:110 , TYR B:113BINDING SITE FOR RESIDUE 30U A 401
02AC2SOFTWAREHIS A:268 , PRO A:271 , SER A:272 , TYR A:273 , HIS A:277 , HIS A:279 , ARG A:294 , PO4 A:404BINDING SITE FOR RESIDUE PO4 A 402
03AC3SOFTWAREHIS A:296 , ASN A:304 , HIS A:311 , TYR A:312 , GLU B:300 , PO4 B:402BINDING SITE FOR RESIDUE PO4 A 403
04AC4SOFTWARELYS A:207 , HIS A:268 , SER A:272 , ARG A:294 , PO4 A:402BINDING SITE FOR RESIDUE PO4 A 404
05AC5SOFTWAREHIS B:268 , PRO B:271 , SER B:272 , HIS B:277 , HIS B:279 , ARG B:294BINDING SITE FOR RESIDUE PO4 B 401
06AC6SOFTWAREGLU A:300 , PO4 A:403 , HIS B:296 , ASN B:304 , TYR B:312BINDING SITE FOR RESIDUE PO4 B 402
07AC7SOFTWAREASP B:187 , ILE B:189 , VAL B:190 , ARG B:255BINDING SITE FOR RESIDUE PO4 B 403
08AC8SOFTWAREHIS C:268 , PRO C:271 , SER C:272 , HIS C:277 , HIS C:279 , ARG C:294BINDING SITE FOR RESIDUE PO4 C 401
09AC9SOFTWAREHIS C:296 , ASN C:304 , HIS C:311 , TYR C:312 , GLU D:300BINDING SITE FOR RESIDUE PO4 C 402
10BC1SOFTWAREPHE C:108 , TYR C:113 , THR D:130 , VAL D:132 , TYR D:143 , TRP D:175 , GLU D:185 , ARG D:188 , PRO D:204 , ASP D:205 , LEU D:206BINDING SITE FOR RESIDUE 30U D 401
11BC2SOFTWAREHIS D:296 , ASN D:304 , TYR D:312BINDING SITE FOR RESIDUE PO4 D 402
12BC3SOFTWAREHIS D:268 , PRO D:271 , SER D:272 , TYR D:273 , HIS D:277 , HIS D:279 , ARG D:294 , GOL D:404BINDING SITE FOR RESIDUE PO4 D 403
13BC4SOFTWARELYS D:207 , SER D:272 , ARG D:294 , PO4 D:403BINDING SITE FOR RESIDUE GOL D 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:133 -Pro A:134
2Tyr B:133 -Pro B:134
3Tyr C:133 -Pro C:134
4Tyr D:133 -Pro D:134

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QDV)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee....eeeeeee...eeeeeee...hhhhhhhhhh....eeeee...eeeeee..hhhhh.eeeeee...hhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhh.eee......eeeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee........eeeeee............eeehhhhhhhhhhh.hhhhhh.eeeeee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qdv A  40 VRLPFSGFRLQKVLRESARDKIIFLHGKVEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQ 336
                                    49        59        78        88        98       108 ||    119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       
                                                       68|                             110|                                                                                                                                                                                                                                
                                                        78                              112                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeee....eeeeeee...eeeeeee...hhhhhhhhhh....eeeeeee..eeeeee..hhhhh.eeeeee...hhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhh.eee......eeeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee........eeeeee............eeehhhhhhhhhhh.hhhhhh.eeeeee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qdv B  40 VRLPFSGFRLQKVLRESARDKIIFLHGKVNDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQ 336
                                    49        59        69|       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        
                                                        69|                                                                                                                                                                                                                                                                 
                                                         79                                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee....eeeeee....eeeeeee...hhhhhhhhhhh...eeeeeee..eeeeee..hhhhh.eeeeee...hhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhh.eee......eeeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee........eeeeee............eeehhhhhhhhhhh.hhhhhh.eeeeee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qdv C  39 PVRLPFSGFRLQKVLRESARDKIIFLHGKGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQ 336
                                    48        58        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327         
                                                       67|                                                                                                                                                                                                                                                                   
                                                        77                                                                                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee....eeeeeeee.....eeeeeeeee...hhhhhhhhh..eee.....eeeeee..hhhhh.eeeeee...hhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhh.eee......eeeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee........eeeeee............eeehhhhhhhhhhh.hhhhhh.eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qdv D  38 APVRLPFSGFRLQKVLRESARDKIIFLHGKVNEGDGEDAVVILEKTPFQVEQVAQLLPELQLQFSDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS 337
                                    47        57        67  ||    81        91      |104    || 115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335  
                                                           70|                     98|    109|                                                                                                                                                                                                                                  
                                                            75                     102     111
   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 4QDV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)

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    Tyr A:133 - Pro A:134   [ RasMol ]  
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  4qdv
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  DCPS_HUMAN | Q96C86
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 Related Entries

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        DCPS_HUMAN | Q96C86: 1st0 1st4 1xml 1xmm 3bl7 3bl9 3bla 4qde 4qeb

(-) Related Entries Specified in the PDB File

4qde 4qeb