Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MPY-RNASE J, AN ARCHAEAL RNASE J FROM METHANOLOBUS PSYCHROPHILUS R15
 
Authors :  N. Feng, D. F. Li
Date :  30 Dec 15  (Deposition) - 04 Jan 17  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Exoribonuclease, Beta-Casp, Mbl, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zheng, N. Feng, D. F. Li, J. Li, X. Z. Dong
Molecular Insights Into Catalysis And Processive Exonucleolytic Mechanisms Of Prokaryotic Rnase J Revealing Striking Parallels With That Of Eukaryotic Xrn1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBONUCLEASE J
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 2-448
    Gene: RNJ, MPSY_0886
    Organism Scientific: METHANOLOBUS PSYCHROPHILUS R15
    Organism Taxid: 1094980
    Synonym: RNASE J

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1SO418Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:86 , ASP A:174 , HIS A:410 , ZN A:502 , HOH A:601binding site for residue ZN A 501
02AC2SOFTWAREHIS A:82 , HIS A:84 , ASP A:86 , HIS A:152 , ASP A:174 , ZN A:501binding site for residue ZN A 502
03AC3SOFTWAREASN A:354 , HIS A:384 , SER A:386 , GLY A:387 , HIS A:388binding site for residue SO4 A 503
04AC4SOFTWARETHR A:244 , PHE A:245 , ALA A:246 , SER A:247 , HIS A:323binding site for residue SO4 A 504
05AC5SOFTWAREGLY A:270 , ARG A:271 , SER A:272 , THR A:321binding site for residue SO4 A 505
06AC6SOFTWAREARG A:271 , SER A:297 , ARG A:298binding site for residue SO4 A 506
07AC7SOFTWAREHIS B:82 , HIS B:84 , HIS B:152 , ASP B:174 , ZN B:502binding site for residue ZN B 501
08AC8SOFTWAREASP B:86 , HIS B:87 , ASP B:174 , HIS B:410 , ZN B:501binding site for residue ZN B 502
09AC9SOFTWAREASN B:354 , HIS B:384 , SER B:386 , GLY B:387 , HIS B:388binding site for residue SO4 B 503
10AD1SOFTWAREPHE B:245 , ALA B:246 , SER B:247 , HIS B:323binding site for residue SO4 B 504
11AD2SOFTWAREGLY B:270 , ARG B:271 , SER B:272 , THR B:321binding site for residue SO4 B 505
12AD3SOFTWAREARG B:271 , SER B:297 , ARG B:298binding site for residue SO4 B 506
13AD4SOFTWAREASN B:213 , ARG B:391binding site for residue SO4 B 507

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:60 -Ala A:61
2Val A:124 -Lys A:125
3Gly B:-4 -Ser B:-3
4Gly B:60 -Ala B:61
5Phe B:122 -Gly B:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HAA)

(-) 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:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeee..eeeee....................hhhhhhhhh...hhhhhhh...eeeeee....hhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh..........eee.....eee.....eeeeeee......eeeeeeee..eeeeee...............hhhhhhhhhhhheeeeeee...........hhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.........eee.hhhhhhhhhhhhhhhh...eeeee........hhhhhhhh...........eeeee.....hhhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...............eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5haa A   1 STEIGIIAVGGYNEMGRNMTAIRVNEDIIIIDMGIRLDRVQIHEDVDTDRMHSLELIEMGAIPDDTIMNEVNGNVRAIVCTHGHLDHIGAIPKLAHRYAAPIIATPYTTALIKHQIDSERKFGVKNNIVALKAGETLEITKDITIEFINTQHSIIDTVFVAIHTPSGAVVYACDFKFDRTPTLGEVPDFDRLKELGKEGVIALITESTNAGRNGKTPSELIAHMMLKDVLLGTEESAVGMIVTTFASHIARVNSIVQFAQEMGRIPVLLGRSMERYVGTAYQLGYIDLPENVEIYGSRRDIDNALKKIMEAGKDKYLPVMTGHQGEPGAVLGRIANGETPFKVETGDRIIFSANVIPNPMTQANRYALETKLKMKGARIYDNVHVSGHAYREDHWELLRMLKPEHVIPAHGTIQMHSEYIQMAEDAGYSLGDTLHLLRNGEELYIEE 447
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       


Chain B from PDB  Type:PROTEIN  Length:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeee........eeeeee..eeeee....................hhhhhhhhh...hhhhhhh...eeeeee....hhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhh.......eee.....eeeee..eeeeeeee......eeeeeeee..eeeeee...............hhhhhhhhhhhheeeeeee...........hhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhh.........eee.hhhhhhhhhhhhhhhh...eeeee........hhhhhhhh...........eeeee.....hhhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh..............eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5haa B -13 HHSSGLVPRGSHSTEIGIIAVGGYNEMGRNMTAIRVNEDIIIIDMGIRLDRVQIHEDVDTDRMHSLELIEMGAIPDDTIMNEVNGNVRAIVCTHGHLDHIGAIPKLAHRYAAPIIATPYTTALIKHQIDSERKFGVKNNIVALKAGETLEITKDITIEFINTQHSIIDTVFVAIHTPSGAVVYACDFKFDRTPTLGEVPDFDRLKELGKEGVIALITESTNAGRNGKTPSELIAHMMLKDVLLGTEESAVGMIVTTFASHIARVNSIVQFAQEMGRIPVLLGRSMERYVGTAYQLGYIDLPENVEIYGSRRDIDNALKKIMEAGKDKYLPVMTGHQGEPGAVLGRIANGETPFKVETGDRIIFSANVIPNPMTQANRYALETKLKMKGARIYDNVHVSGHAYREDHWELLRMLKPEHVIPAHGTIQMHSEYIQMAEDAGYSLGDTLHLLRNGEELYIEED 448
                                    -4 ||      8        18        28        38        48        58        68        78        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       338       348       358       368       378       388       398       408       418       428       438       448
                                      -2|                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                        1
   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 5HAA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:60 - Ala A:61   [ RasMol ]  
    Gly B:-4 - Ser B:-3   [ RasMol ]  
    Gly B:60 - Ala B:61   [ RasMol ]  
    Phe B:122 - Gly B:123   [ RasMol ]  
    Val A:124 - Lys A:125   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5haa
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  K4MAF9_9EURY | K4MAF9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.1.-.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  K4MAF9_9EURY | K4MAF9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        K4MAF9_9EURY | K4MAF9: 5hab

(-) Related Entries Specified in the PDB File

5hab