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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE X-RAY STRUCTURE OF ZEBRAFISH RNASE1 FROM A NEW CRYSTAL FORM AT PH 4.5
 
Authors :  I. Russo Krauss, A. Merlino, L. Mazzarella, F. Sica
Date :  26 Jan 10  (Deposition) - 08 Dec 10  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Angiogenins, Fish Rnases, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Pizzo, A. Merlino, M. Turano, I. Russo Krauss, F. Coscia, A. Zanfardino, M. Varcamonti, A. Furia, C. Giancola, L. Mazzarella, F. Sica, G. D'Alessio
A New Rnase Sheds Light On The Rnase/Angiogenin Subfamily From Zebrafish.
Biochem. J. V. 433 345 2010
PubMed-ID: 21050179  |  Reference-DOI: 10.1042/BJ20100892
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZEBRAFISH RNASE1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO44Ligand/IonSULFATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:74 , HIS A:119 , HIS A:121 , HOH A:3063BINDING SITE FOR RESIDUE SO4 A 3000
2AC2SOFTWAREARG A:106 , TYR A:107 , HOH A:3114 , HOH A:3145 , HOH A:5022 , ARG B:66 , HOH B:3173BINDING SITE FOR RESIDUE SO4 A 3001
3AC3SOFTWAREGLY A:18 , PRO A:19 , ASP A:20 , MET A:21 , ARG A:25 , GLU A:29 , ARG A:35 , ARG A:66 , HOH A:3211 , HOH A:3270BINDING SITE FOR RESIDUE SO4 A 3002
4AC4SOFTWAREASN A:73 , LYS A:111 , HOH A:3236 , HOH A:3259 , HOH A:5030 , HOH A:5085BINDING SITE FOR RESIDUE SO4 A 3006
5AC5SOFTWAREGLY B:18 , PRO B:19 , ASP B:20 , MET B:21 , ARG B:25 , GLU B:29 , ARG B:35 , HOH B:3222BINDING SITE FOR RESIDUE ACT B 5000
6AC6SOFTWAREASN A:27 , GLU A:98 , HOH A:3022 , HOH A:3069 , ARG B:106 , TYR B:107 , HOH B:3066 , HOH B:3072BINDING SITE FOR RESIDUE SO4 B 3003
7AC7SOFTWAREMET A:3 , ASN A:126 , LYS B:6 , ASP B:43 , ASN B:44 , ARG B:93 , HOH B:3116 , HOH B:3178 , HOH B:3261 , HOH B:5037BINDING SITE FOR RESIDUE SO4 B 3004
8AC8SOFTWARELYS A:10 , ARG B:100 , HOH B:3028 , HOH B:3123 , HOH B:3244 , HOH B:3265 , HOH B:3301BINDING SITE FOR RESIDUE SO4 B 3005
9AC9SOFTWAREASP A:123 , GLU A:124 , GLU B:114 , HOH B:3100 , HOH B:3209 , HOH B:3268BINDING SITE FOR RESIDUE SO4 B 3007

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:26 -A:86
2A:46 -A:97
3A:64 -A:112
4B:26 -B:86
5B:46 -B:97
6B:64 -B:112

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:94 -Pro A:95
2His B:94 -Pro B:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LJD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LJD)

(-) Exons   (0, 0)

(no "Exon" information available for 3LJD)

(-) 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:126
 aligned with E7FH76_DANRE | E7FH76 from UniProtKB/TrEMBL  Length:126

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
         E7FH76_DANRE     1 MHVKERYKNFLNQHVGPDMSVQRCNSEIGPNNRKITLSGTDNGCKPVNTFILANKRLIKTVCGRAGSPQGNMVRSNQPFPVVKCVLNNGERHPYCEYRGTRSTRYIVLKCEEGWPVHYHEDEVNVG 126
               SCOP domains d3ljda_ A: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhh.................eeeee..hhhhhhhhhh..eeee..eeee...eeeeeeeeee.......eeeeeeeee..eeeee..eeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ljd A   3 MHVKERYKNFLNQHVGPDMSVQRCNSEIGPNNRKITLSGTDNGCKPVNTFILANKRLIKTVCGRAGSPQGNMVRSNQPFPVVKCVLNNGERHPYCEYRGTRSTRYIVLKCEEGWPVHYHEDEVNVG 128
                                    12        22        32        42        52        62        72        82        92       102       112       122      


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with E7FH76_DANRE | E7FH76 from UniProtKB/TrEMBL  Length:126

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
         E7FH76_DANRE     1 MHVKERYKNFLNQHVGPDMSVQRCNSEIGPNNRKITLSGTDNGCKPVNTFILANKRLIKTVCGRAGSPQGNMVRSNQPFPVVKCVLNNGERHPYCEYRGTRSTRYIVLKCEEGWPVHYHEDEVNVG 126
               SCOP domains d3ljdb_ B: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhh.................eeeee..hhhhhhhhhh..eeee..eeee...eeeeeeeeee.......eeeeeeeee..eeeee..eeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ljd B   3 MHVKERYKNFLNQHVGPDMSVQRCNSEIGPNNRKITLSGTDNGCKPVNTFILANKRLIKTVCGRAGSPQGNMVRSNQPFPVVKCVLNNGERHPYCEYRGTRSTRYIVLKCEEGWPVHYHEDEVNVG 128
                                    12        22        32        42        52        62        72        82        92       102       112       122
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LJD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LJD)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (E7FH76_DANRE | E7FH76)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
    His A:94 - Pro A:95   [ RasMol ]  
    His B:94 - Pro B:95   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3ljd
    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
  E7FH76_DANRE | E7FH76
    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)
  (no 'Enzyme Classificator' available)
    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
  E7FH76_DANRE | E7FH76
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        E7FH76_DANRE | E7FH76: 3ln8

(-) Related Entries Specified in the PDB File

2vq8 THE X-RAY STRUCTURE OF ZEBRAFISH RNASE 1
2vq9 THE X-RAY STRUCTURE OF ZEBRAFISH RNASE 3
3lje THE X-RAY STRUCTURE OF ZEBRAFISH RNASE5
3ln8 THE X-RAY STRUCTURE OF ZF-RNASE-1 FROM A NEW CRYSTAL FORM AT PH 7.3