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(-) Description

Title :  TARG1 (C6ORF130), TERMINAL ADP-RIBOSE GLYCOHYDROLASE 1 ADP-RIBOSE COMPLEX
 
Authors :  M. J. Schellenberg, C. D. Appel, J. Krahn, R. S. Williams
Date :  09 Feb 13  (Deposition) - 27 Mar 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Dna Repair, Cellular Signaling, Macro Domain, Glycohydrolase, Poly- Adp Ribose, Parp, Adp-Ribose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sharifi, R. Morra, C. D. Appel, M. Tallis, B. Chioza, G. Jankevicius M. A. Simpson, I. Matic, E. Ozkan, B. Golia, M. J. Schellenberg, R. Weston, J. G. Williams, M. N. Rossi, H. Galehdari, J. Krahn, A. Wan, R. C. Trembath, A. H. Crosby, D. Ahel, R. Hay, A. G. Ladurner, G. Timinszky, R. S. Williams, I. Ahel
Deficiency Of Terminal Adp-Ribose Protein Glycohydrolase Targ1/C6Orf130 In Neurodegenerative Disease.
Embo J. V. 32 1225 2013
PubMed-ID: 23481255  |  Reference-DOI: 10.1038/EMBOJ.2013.51

(-) Compounds

Molecule 1 - O-ACETYL-ADP-RIBOSE DEACETYLASE 1
    Chains: A, B, C, D
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: OARD1, C6ORF130
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
1BO41Ligand/IonBORATE ION
2CL4Ligand/IonCHLORIDE ION
3EDO19Ligand/Ion1,2-ETHANEDIOL
4SBE1Ligand/Ion1,3,2-DIOXABOROLAN-2-OL
5ZZC4Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1BO41Ligand/IonBORATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4SBE-1Ligand/Ion1,3,2-DIOXABOROLAN-2-OL
5ZZC1Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1BO4-1Ligand/IonBORATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO7Ligand/Ion1,2-ETHANEDIOL
4SBE1Ligand/Ion1,3,2-DIOXABOROLAN-2-OL
5ZZC1Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1BO4-1Ligand/IonBORATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4SBE-1Ligand/Ion1,3,2-DIOXABOROLAN-2-OL
5ZZC1Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE
Biological Unit 4 (2, 5)
No.NameCountTypeFull Name
1BO4-1Ligand/IonBORATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4SBE-1Ligand/Ion1,3,2-DIOXABOROLAN-2-OL
5ZZC1Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:23 , LEU A:24 , CYS A:36 , ILE A:37 , GLY A:46 , ILE A:47 , LYS A:87 , PRO A:121 , ARG A:122 , GLY A:124 , CYS A:125 , GLY A:126 , LEU A:127 , ASP A:128 , LEU A:155 , BO4 A:202 , HOH A:307 , HOH A:310 , HOH A:315 , HOH A:342 , HOH A:352 , HOH A:465 , HOH A:487 , HOH A:489 , HOH A:491BINDING SITE FOR RESIDUE ZZC A 201
02AC2SOFTWAREZZC A:201 , HOH A:317BINDING SITE FOR RESIDUE BO4 A 202
03AC3SOFTWARESER A:38 , ARG A:42 , MET A:43BINDING SITE FOR RESIDUE CL A 203
04AC4SOFTWAREGLU A:39 , CYS A:41 , LEU A:61 , GLN A:65 , LYS A:66 , HOH A:386BINDING SITE FOR RESIDUE EDO A 204
05AC5SOFTWAREPHE A:25 , CYS A:27 , PRO A:28 , LYS A:29 , LYS A:54 , ARG A:79BINDING SITE FOR RESIDUE EDO A 205
06AC6SOFTWAREGLY A:78 , ARG A:79 , TYR A:80 , ASN A:113 , GLY A:114 , HOH A:308 , HOH A:327 , HOH A:351BINDING SITE FOR RESIDUE EDO A 206
07AC7SOFTWAREASN A:134 , ALA A:137 , HOH A:340 , HOH A:475BINDING SITE FOR RESIDUE EDO A 207
08AC8SOFTWARELYS A:53 , LYS A:54 , HOH A:427 , CYS B:27 , PRO B:28 , LYS B:29BINDING SITE FOR RESIDUE EDO A 208
09AC9SOFTWAREPRO A:28 , ASP A:31 , HOH A:316 , HOH A:328 , HOH A:363 , HOH A:387 , HOH A:517 , LYS C:52BINDING SITE FOR RESIDUE EDO A 209
10BC1SOFTWAREASP B:23 , LEU B:24 , CYS B:36 , ILE B:37 , SER B:38 , GLY B:46 , ILE B:47 , THR B:86 , LYS B:87 , ALA B:90 , PRO B:121 , ARG B:122 , GLY B:124 , CYS B:125 , GLY B:126 , LEU B:127 , ASP B:128 , LEU B:155 , SBE B:202 , HOH B:309 , HOH B:314 , HOH B:318 , HOH B:374 , HOH B:426BINDING SITE FOR RESIDUE ZZC B 201
11BC2SOFTWAREARG B:122 , ZZC B:201 , HOH B:358 , HOH B:454BINDING SITE FOR RESIDUE SBE B 202
12BC3SOFTWARESER B:38 , ARG B:42 , MET B:43 , HOH B:374BINDING SITE FOR RESIDUE CL B 203
13BC4SOFTWAREPHE B:25 , CYS B:27 , PRO B:28 , LYS B:29 , LYS B:54 , ARG B:79 , HOH B:416BINDING SITE FOR RESIDUE EDO B 204
14BC5SOFTWAREPRO B:28 , ASP B:31 , SER B:119 , THR B:151 , TYR B:153 , HOH B:323 , HOH B:412 , HOH B:441BINDING SITE FOR RESIDUE EDO B 205
15BC6SOFTWAREGLY B:114 , HOH B:422BINDING SITE FOR RESIDUE EDO B 206
16BC7SOFTWARELYS B:66 , VAL B:71 , VAL B:73 , HOH B:317 , HOH B:320 , HOH B:370BINDING SITE FOR RESIDUE EDO B 207
17BC8SOFTWAREGLU B:39 , CYS B:41 , LEU B:61 , GLN B:65 , LYS B:66 , HOH B:359BINDING SITE FOR RESIDUE EDO B 208
18BC9SOFTWARETHR B:95 , TYR B:96 , GLU B:97BINDING SITE FOR RESIDUE EDO B 209
19CC1SOFTWAREASN B:134BINDING SITE FOR RESIDUE EDO B 210
20CC2SOFTWAREASP C:23 , LEU C:24 , CYS C:36 , ILE C:37 , GLY C:46 , ILE C:47 , LYS C:87 , ALA C:90 , PRO C:121 , ARG C:122 , GLY C:124 , CYS C:125 , GLY C:126 , LEU C:127 , ASP C:128 , TYR C:153 , HOH C:315 , HOH C:316 , HOH C:318 , HOH C:370 , HOH C:375 , HOH C:399 , HOH C:411BINDING SITE FOR RESIDUE ZZC C 201
21CC3SOFTWARESER C:38 , ARG C:42 , MET C:43BINDING SITE FOR RESIDUE CL C 202
22CC4SOFTWAREPHE C:25 , CYS C:27 , PRO C:28 , LYS C:29 , LYS C:54 , ARG C:79 , HOH C:373BINDING SITE FOR RESIDUE EDO C 203
23CC5SOFTWAREGLU C:39 , CYS C:41 , LEU C:61 , GLN C:65 , LYS C:66 , HOH C:354BINDING SITE FOR RESIDUE EDO C 204
24CC6SOFTWAREASP D:23 , LEU D:24 , CYS D:36 , ILE D:37 , GLY D:46 , ILE D:47 , LYS D:87 , ALA D:90 , PRO D:121 , ARG D:122 , GLY D:124 , CYS D:125 , GLY D:126 , LEU D:127 , ASP D:128 , TYR D:153 , HOH D:309 , HOH D:310 , HOH D:314 , HOH D:331 , HOH D:380 , HOH D:388 , HOH D:411 , HOH D:413 , HOH D:437BINDING SITE FOR RESIDUE ZZC D 201
25CC7SOFTWARESER D:38 , ARG D:42 , MET D:43BINDING SITE FOR RESIDUE CL D 202
26CC8SOFTWARECYS D:27 , PRO D:28 , LYS D:29 , LYS D:54 , ARG D:79BINDING SITE FOR RESIDUE EDO D 203
27CC9SOFTWAREGLU D:39 , CYS D:41 , LEU D:61 , GLN D:65 , LYS D:66 , HOH D:358BINDING SITE FOR RESIDUE EDO D 204
28DC1SOFTWAREGLY D:78 , ARG D:79 , TYR D:80 , ASN D:113 , GLY D:114 , HOH D:306 , HOH D:323BINDING SITE FOR RESIDUE EDO D 205
29DC2SOFTWARELYS D:66 , VAL D:71 , VAL D:73 , HOH D:320 , HOH D:337 , HOH D:417BINDING SITE FOR RESIDUE EDO D 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J5S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J5S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J5S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J5S)

(-) Exons   (0, 0)

(no "Exon" information available for 4J5S)

(-) 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:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.hhhhh....eeeeeee.......hhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5s A  10 GSHMGSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLEAMKSHCLKNGVTDLSMPRIGCGLDRLQWENVSAMIEEVFEATDIKITVYTL 155
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149      


Chain B from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhh....eeeeeee.......hhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5s B  15 SRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLEAMKSHCLKNGVTDLSMPRIGCGLDRLQWENVSAMIEEVFEATDIKITVYTL 155
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154 


Chain C from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhh....eeeeee........hhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeeee.........hhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5s C  16 RITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLEAMKSHCLKNGVTDLSMPRIGCGLDRLQWENVSAMIEEVFEATDIKITVYTL 155
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155


Chain D from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhh....eeeeeee........hhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5s D  16 RITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLEAMKSHCLKNGVTDLSMPRIGCGLDRLQWENVSAMIEEVFEATDIKITVYTL 155
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155
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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 4J5S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J5S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J5S)

(-) Gene Ontology  (5, 5)

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 Related Entries

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

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        OARD1_HUMAN | Q9Y530: 2eee 2l8r 2lgr 4j5q 4j5r

(-) Related Entries Specified in the PDB File

4j5q 4j5r