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(-) Description

Title :  CRYSTAL STRUCTURE OF PORCINE RNASE 4 IN COMPLEX WITH DUMP
 
Authors :  S. Liang, K. R. Acharya
Date :  25 Sep 15  (Deposition) - 20 Jan 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
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 :  Ribonuclease 4, Hydrolase, Rna Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liang, K. R. Acharya
Structural Basis Of Substrate Specificity In Porcine Rnase 4.
Febs J. V. 283 912 2016
PubMed-ID: 26748441  |  Reference-DOI: 10.1111/FEBS.13646

(-) Compounds

Molecule 1 - RIBONUCLEASE 4
    Chains: A, B, C, D
    EC Number: 3.1.27.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 29-147
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: RNASE 4, RIBONUCLEASE PL3

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2UMP4Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
2UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
2UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:7 , GLN A:11 , HIS A:12 , LYS A:40 , PHE A:42 , ASN A:43 , THR A:44 , HIS A:116 , PHE A:117 , LYS A:119BINDING SITE FOR RESIDUE UMP A1120
2AC2SOFTWAREARG B:7 , GLN B:11 , HIS B:12 , LYS B:40 , PHE B:42 , ASN B:43 , THR B:44 , HIS B:116 , PHE B:117 , LYS B:119 , HOH B:2004 , TRP C:51 , PRO C:111BINDING SITE FOR RESIDUE UMP B1120
3AC3SOFTWAREARG C:7 , GLN C:11 , HIS C:12 , LYS C:40 , PHE C:42 , THR C:44 , HIS C:116 , PHE C:117 , ASP C:118 , LYS C:119 , HOH C:2004 , HOH C:2005BINDING SITE FOR RESIDUE UMP C1120
4AC4SOFTWARESER A:55 , ARG D:7 , GLN D:11 , HIS D:12 , LYS D:40 , PHE D:42 , HIS D:116 , PHE D:117 , ASP D:118 , HOH D:2006BINDING SITE FOR RESIDUE UMP D1120
5AC5SOFTWAREARG B:31 , ARG B:32 , ARG D:31 , ARG D:32BINDING SITE FOR RESIDUE PO4 B1121
6AC6SOFTWAREARG A:31 , ARG A:32 , HOH A:2009 , ARG C:31 , ARG C:32BINDING SITE FOR RESIDUE PO4 A1121

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:25 -A:81
2A:39 -A:92
3A:57 -A:107
4A:64 -A:71
5B:25 -B:81
6B:39 -B:92
7B:57 -B:107
8B:64 -B:71
9C:25 -C:81
10C:39 -C:92
11C:57 -C:107
12C:64 -C:71
13D:25 -D:81
14D:39 -D:92
15D:57 -D:107
16D:64 -D:71

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:89 -Pro A:90
2Asn A:110 -Pro A:111
3Ala B:89 -Pro B:90
4Asn B:110 -Pro B:111
5Ala C:89 -Pro C:90
6Asn C:110 -Pro C:111
7Ala D:89 -Pro D:90
8Asn D:110 -Pro D:111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ARK)

(-) 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:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.......hhhhhhhhhhhh.........eeeee..hhhhhhhhhhh...........eeeeeeeeeeeee..........eeeeeeeeeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5ark A   1 QDRMYQRFLRQHVDPDATGGNDAYCNLMMQRRKMTSHYCKRFNTFIHEDIWNIRSICSTSNIQCKNGQMNCHEGVVKVTDCRETGSSRAPNCRYRAMASTRRVVIACEGNPEVPVHFDK 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain B from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.......hhhhhhhhhhhh.........eeeee..hhhhhhhhh.............eeeeeeeeeeeee..........eeeeeeeeeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5ark B   1 QDRMYQRFLRQHVDPDATGGNDAYCNLMMQRRKMTSHYCKRFNTFIHEDIWNIRSICSTSNIQCKNGQMNCHEGVVKVTDCRETGSSRAPNCRYRAMASTRRVVIACEGNPEVPVHFDK 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain C from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.......hhhhhhhhhhhh.........eeeee..hhhhhhhhhhh...........eeeeeeeeeeeee..........eeeeeeeeeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5ark C   1 QDRMYQRFLRQHVDPDATGGNDAYCNLMMQRRKMTSHYCKRFNTFIHEDIWNIRSICSTSNIQCKNGQMNCHEGVVKVTDCRETGSSRAPNCRYRAMASTRRVVIACEGNPEVPVHFDK 119
                                    10        20        30        40        50        60        70        80        90       100       110         


Chain D from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.......hhhhhhhhhhhh.........eeeee..hhhhhhhhhhh...........eeeeeeeeeeeee..........eeeeeeeeeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5ark D   1 QDRMYQRFLRQHVDPDATGGNDAYCNLMMQRRKMTSHYCKRFNTFIHEDIWNIRSICSTSNIQCKNGQMNCHEGVVKVTDCRETGSSRAPNCRYRAMASTRRVVIACEGNPEVPVHFDK 119
                                    10        20        30        40        50        60        70        80        90       100       110
   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 5ARK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Asn A:110 - Pro A:111   [ RasMol ]  
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  3.1.27.-
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 Related Entries

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

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        RNAS4_PIG | P15468: 5ar6 5arj 5arl

(-) Related Entries Specified in the PDB File

5ar6 CRYSTAL STRUCTURE OF PORCINE RNASE 4
5arj CRYSTAL STRUCTURE OF PORCINE RNASE 4 D80A MUTANT
5arl CRYSTAL STRUCTURE OF PORCINE RNASE 4 D80A MUTANT IN COMPLEX WITH DCMP