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(-) Description

Title :  APO DBR1
 
Authors :  N. E. Clark, A. B. Taylor, P. J. Hart
Date :  25 May 16  (Deposition) - 07 Dec 16  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Metalloenzyme, Apo-Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. E. Clark, A. Katolik, K. Roberts, A. B. Taylor, S. P. Holloway, J. P. Schuermann, E. J. Montemayor, S. W. Stevens, P. F. Fitzpatrick, M. J. Damha, P. J. Hart
The Rna Lariat Debranching Enzyme Dbr1: Metal Dependence An Branched Rna Co-Crystal Structures
Proc. Natl. Acad. Sci. Usa 2016
PubMed: search  |  Reference-DOI: 10.1073/PNAS.1612729114

(-) Compounds

Molecule 1 - RNA LARIAT DEBRANCHING ENZYME, PUTATIVE
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: EHI_062730
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1SO416Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:50 , ASN A:95 , HIS A:99 , PRO A:146binding site for residue SO4 A 601
02AC2SOFTWAREASN A:90 , HIS A:91 , HIS A:230 , HIS A:232 , HOH A:711binding site for residue SO4 A 602
03AC3SOFTWAREGLN A:163 , SER A:298 , ILE A:299 , SER A:300binding site for residue SO4 A 603
04AC4SOFTWAREARG B:50 , ASN B:95 , HIS B:99 , PRO B:146 , HOH B:708 , HOH B:760binding site for residue SO4 B 601
05AC5SOFTWAREASN B:90 , HIS B:91 , HIS B:230 , HIS B:232binding site for residue SO4 B 602
06AC6SOFTWARELYS B:59 , ILE B:132 , LYS B:134 , PHE B:155 , HIS B:156 , HOH B:702binding site for residue SO4 B 603
07AC7SOFTWAREARG C:50 , ASN C:95 , HIS C:99 , PRO C:146 , HOH C:707 , HOH C:711 , HOH C:722 , HOH C:763binding site for residue SO4 C 601
08AC8SOFTWARETHR B:307 , LYS B:308 , LYS C:215binding site for residue SO4 C 602
09AC9SOFTWARELYS C:320 , TYR C:321 , HOH C:721 , TYR D:74 , THR D:332binding site for residue SO4 C 603
10AD1SOFTWAREASN C:90 , HIS C:91 , HIS C:232binding site for residue SO4 C 604
11AD2SOFTWARELYS B:215 , THR C:307 , LYS C:308 , HOH C:782binding site for residue SO4 C 605
12AD3SOFTWAREARG D:50 , ASN D:95 , HIS D:99 , PRO D:146 , HOH D:708binding site for residue SO4 D 601
13AD4SOFTWAREASN D:90 , HIS D:91 , HIS D:230 , HIS D:232 , HOH D:702binding site for residue SO4 D 602
14AD5SOFTWAREILE D:132 , LYS D:134 , PHE D:155 , HIS D:156binding site for residue SO4 D 603
15AD6SOFTWAREASN E:90 , HIS E:91 , HIS E:232 , HOH E:511binding site for residue SO4 E 401
16AD7SOFTWAREARG E:50 , ASN E:95 , HIS E:99 , HOH E:521 , HOH E:534binding site for residue SO4 E 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K71)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Tyr A:144 -Pro A:145
2Phe A:292 -Pro A:293
3Tyr B:144 -Pro B:145
4Phe B:292 -Pro B:293
5Tyr C:144 -Pro C:145
6Phe C:292 -Pro C:293
7Tyr D:144 -Pro D:145
8Phe D:292 -Pro D:293
9Tyr E:144 -Pro E:145
10Phe E:292 -Pro E:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K71)

(-) Exons   (0, 0)

(no "Exon" information available for 5K71)

(-) 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhh...eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhhhh......hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.........eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k71 A   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        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         


Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhhhh......hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.........eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k71 B   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        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         


Chain C from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhhhh......hhhhhhh.........eee......hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.........eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k71 C   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        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         


Chain D from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhhhh......hhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.....hhh.eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k71 D   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        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         


Chain E from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhhhh......hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.........eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k71 E   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        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
   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 5K71)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K71)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K71)

(-) Gene Ontology  (6, 6)

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 Related Entries

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

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        C4M1P9_ENTHI | C4M1P9: 4pef 4peg 4peh 4pei 5k73 5k77 5k78

(-) Related Entries Specified in the PDB File

5k73 5k77 5k78