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(-) Description

Title :  CRYSTAL STRUCTURE OF SCHEFFERSOMYCES STIPITIS RAI1 IN COMPLEX WITH (3'-NADP)+ AND CALCIUM ION
 
Authors :  S. K. Doamekpor, L. Tong
Date :  24 Jan 17  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
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 :  Hydrolase, Nadp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Jiao, S. K. Doamekpor, J. G. Bird, B. E. Nickels, L. Tong, R. P. Hart, M. Kiledjian
5' End Nicotinamide Adenine Dinucleotide Cap In Human Cells Promotes Rna Decay Through Dxo-Mediated Denadding.
Cell V. 168 1015 2017
PubMed-ID: 28283058  |  Reference-DOI: 10.1016/J.CELL.2017.02.019

(-) Compounds

Molecule 1 - RAI1
    Chains: A, B, C, D
    Engineered: YES
    Organism Common: YEAST
    Organism Scientific: SCHEFFERSOMYCES STIPITIS (STRAIN ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545)
    Organism Taxid: 322104
    Synonym: RAI1

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
10WD2Ligand/Ion[[(2R,3S,4R,5R)-5-(3-AMINOCARBONYL-4H-PYRIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHYL HYDROGENPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3PPV2Ligand/IonPYROPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10WD1Ligand/Ion[[(2R,3S,4R,5R)-5-(3-AMINOCARBONYL-4H-PYRIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHYL HYDROGENPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3PPV-1Ligand/IonPYROPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10WD1Ligand/Ion[[(2R,3S,4R,5R)-5-(3-AMINOCARBONYL-4H-PYRIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHYL HYDROGENPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3PPV-1Ligand/IonPYROPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
10WD-1Ligand/Ion[[(2R,3S,4R,5R)-5-(3-AMINOCARBONYL-4H-PYRIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHYL HYDROGENPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3PPV1Ligand/IonPYROPHOSPHATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
10WD-1Ligand/Ion[[(2R,3S,4R,5R)-5-(3-AMINOCARBONYL-4H-PYRIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHYL HYDROGENPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3PPV1Ligand/IonPYROPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:179 , ASP A:230 , GLU A:249 , LEU A:250 , 0WD A:402 , HOH A:504 , HOH A:505 , HOH A:512binding site for residue CA A 401
2AC2SOFTWAREASN A:76 , MET A:77 , TYR A:107 , ARG A:108 , GLY A:109 , TYR A:176 , GLN A:209 , ALA A:226 , GLY A:227 , GLU A:228 , LYS A:251 , GLN A:275 , CA A:401 , HOH A:522 , HOH A:543 , HOH A:669binding site for residue 0WD A 402
3AC3SOFTWAREASP B:230 , GLU B:249 , LEU B:250 , 0WD B:402 , HOH B:521 , HOH B:540 , HOH B:604binding site for residue CA B 401
4AC4SOFTWAREGLU B:73 , ASN B:76 , MET B:77 , TYR B:107 , ARG B:108 , GLY B:109 , SER B:140 , GLU B:145 , TYR B:176 , ASN B:206 , GLN B:209 , GLY B:227 , GLU B:228 , GLU B:249 , LYS B:251 , CA B:401 , HOH B:503 , HOH B:506 , HOH B:520 , HOH B:521 , HOH B:525 , HOH B:551 , HOH B:560 , HOH B:601 , HOH B:604 , HOH B:617 , HOH B:658 , HOH B:689 , HOH B:691binding site for residue 0WD B 402
5AC5SOFTWAREARG C:108 , GLY C:109 , GLY C:227 , GLU C:228 , HOH C:513binding site for residue PPV C 401
6AC6SOFTWARETYR D:107 , ARG D:108 , GLY D:109 , ALA D:226 , GLY D:227 , GLU D:228 , GLN D:275 , HOH D:517binding site for residue PPV D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:321 -Gly B:322

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ULJ)

(-) 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:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..............eeeeeeee.....ee.hhhhhhhhh..ee..hhhhh........hhhhh...........hhhhhhhhhhhhhhh.........eeeehhhhhhhhhhhhh....eeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhh...........eeeeeeeeee..eeeeeeeee.ee.........hhhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..hhhhhhhh......hhhhhhhhhhhhhhhhhhhh.......eeeeeee....eeeeee...hhhhhhh.....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ulj A   2 MKTLSLQSRAKTTALKQPKEIFAFARDIDGEFVYDQKIVKDENVSYYYLPDSKIDGSIDLQAGYAKFKKIPEEKNMSDMKCLLTALTKYEQEHNNGEKVNVDIITYRGLMTKLLALPYNLNDPVDLNVLAYDGQLFINSDEEIELARRKEEDEHKQQSMTPEKYDHMKRCEFSGYKFEAIATLPKPWADCSRQQIMVNNYEQYISVIKTGIGEAKMLLAGEVDCVWDYIPEDGKDVLSHYMELKTTRILESNGQVVNFEKKLFKTWAQCFLMGIRKVVYGFRDDSFFLRDVELYKTEEIPLLIKNNALGKINCTTALKWYGAVIEWLLQEIPRDDTSKAYRVSFDPSTRTFTLRELMGNENSRLRNGEMLTSEFKQWRESI 394
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191    || 207       217       227       237       247       257       267       277       287       297       307       323       333       343       353       363       373       383       393 
                                                                                                                                                                                                                            196|                                                                                                             315|                                                                        
                                                                                                                                                                                                                             203                                                                                                              322                                                                        


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..........eeeeeeee.....ee.hhhhhhhhh..ee..hhhhh........hhhhh...hhhhh...hhhhhhhhhhhhhhh.........eeeehhhhhhhhhhhhh....eeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.............eeeeeeeeee..eeeeeeee..ee..........hhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........eeeeee....eeeeee...hhhhhhh.....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ulj B  -6 LVPRGSHMMKTLSLQSRAKKQPKEIFAFARDIDGEFVYDQKIVKDENVSYYYLPDSKIDGSIDLQAGYAKFKKIPEEKNMSDMKCLLTALTKYEQEHNNGEKVNVDIITYRGLMTKLLALPYNLNDPVDLNVLAYDGQLFINSDEEIELARRKEEDEHKQQSMTPEKYDHMKRCEFSGYKFEAIATLPKPWAKKMVNNYEQYISVIKTGIGEAKMLLAGEVDCVWDYIPEDGKDVLSHYMELKTTRILESNGQVVNFEKKLFKTWAQCFLMGIRKVVYGFRDDSFFLRDVELYKTEEIPLLIKNNALTENKSGGKINCTTALKWYGAVIEWLLQEIPRDDTSKAYRVSFDPSTRTFTLRELMGNENSRLRNGEMLTSEFKQWRESI 394
                                     3        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 ||    208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388      
                                             12|                                                                                                                                                                         189|                                                                                                                                                                                                 
                                              17                                                                                                                                                                          201                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..............eeeeeeee.....ee.hhhhhhhhh..ee..hhhhh................hhhhh..hhhhhhhhhhhhhhhh.........eeeehhhhhhhhhhhhh....eeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhee..hhhhh.hhhhhh..........eeeeeeeeee..eeeeeeee..ee......hhhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhh.......eeeeeee....eeeeee.hhhhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ulj C   2 MKTLSLQSRAKTTALKQPKEIFAFARDIDGEFVYDQKIVKDENVSYYYLPDSKIDGSIDLQAGYAKFKKIPEEKNMSDMKCLLTALTKYEQEHNNGEKVNVDIITYRGLMTKLLALPYNLNDPVDLNVLAYDGQLFINSDEEIELARRKEEDEHKQQSMTPEKYDHMKRCEFSGYKFEAIATLPKPWADCSRQQIDKRGKKMVNNYEQYISVIKTGIGEAKMLLAGEVDCVWDYIPKDVLSHYMELKTTRILESNGQVVNFEKKLFKTWAQCFLMGIRKVVYGFRDDSFFLRDVELYKTEEIPLLIKNNKINCTTALKWYGAVIEWLLQEIPRDDTSKAYRVSFDPSTRTFTLRELMGNENSRLRNGEMLTSEFKQWRESI 394
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     ||244       254       264       274       284       294       304       323       333       343       353       363       373       383       393 
                                                                                                                                                                                                                                                                     237|                                                                     313|                                                                       
                                                                                                                                                                                                                                                                      241                                                                      323                                                                       


Chain D from PDB  Type:PROTEIN  Length:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..........eeeeeeee.....ee.hhhhhhhhh..ee..hhhhh................hhhhhh.hhhhhhhhhhhhhhhh.........eeeehhhhhhhhhhhhh....eeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeee..ee.........hhhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee.hhhhhh.....hhhhhhhhhhhhhhhhhhhh.......eeeeeee....eeeeee.hhhhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ulj D   2 MKTLSLQSRAKKQPKEIFAFARDIDGEFVYDQKIVKDENVSYYYLPDSKIDGSIDLQAGYAKFKKIPEEKNMSDMKCLLTALTKYEQEHNNGEKVNVDIITYRGLMTKLLALPYNLNDPVDLNVLAYDGQLFINSDEEIELARRKEEDEHKQQSMTPEKYDHMKRCEFSGYKFEAIATLPKPWADCSRQQIDKRGKKMVNNYEQYISVIKTGIGEAKMLLAGEVDCVWDYIPEDGKDVLSHYMELKTTRILESNGQVVNFEKKLFKTWAQCFLMGIRKVVYGFRDDSFFLRDVELYKTEEIPLLIKNKINCTTALKWYGAVIEWLLQEIPRDDTSKAYRVSFDPSTRTFTLRELMGNENSRLRNGEMLTSEFKQWRESI 394
                                    11||      25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305      |325       335       345       355       365       375       385         
                                     12|                                                                                                                                                                                                                                                                                                    312|                                                                       
                                      17                                                                                                                                                                                                                                                                                                     323
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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 5ULJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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