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 :  CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH GUANOSINE-2'-CYCLOPHOSPHATE
 
Authors :  J. Sevcik, V. Bauerova-Hlinkova
Date :  16 Jun 08  (Deposition) - 16 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ribonuclease, Hydrolase, Protein-Mononucleotide Complex, Guanosine- 2'-Monophosphate, Mononucleotide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Bauerova-Hlinkova, R. Dvorsky, D. Perecko, F. Povazanec, J. Sevci
Structure Of Rnase Sa2 Complexes With Mononucleotides - New Aspects Of Catalytic Reaction And Substrate Recognition
Febs J. V. 276 4156 2009
PubMed-ID: 19558492  |  Reference-DOI: 10.1111/J.1742-4658.2009.07125.X

(-) Compounds

Molecule 1 - RIBONUCLEASE
    Chains: A, B, C
    EC Number: 3.1.4.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEH200
    Expression System Strain: NOVA BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES AUREOFACIENS
    Organism Taxid: 1894
    Strain: R8/26
    Synonym: RIBONUCLEASE SA2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
12GP1Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2BGC1Ligand/IonBETA-D-GLUCOSE
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
12GP-1Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2BGC1Ligand/IonBETA-D-GLUCOSE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
12GP1Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2BGC-1Ligand/IonBETA-D-GLUCOSE
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
12GP-1Ligand/IonGUANOSINE-2'-MONOPHOSPHATE
2BGC-1Ligand/IonBETA-D-GLUCOSE
3SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:31 , TYR A:32 , ASN A:33 , ARG A:34 , HOH A:173 , HOH A:198 , GLU B:40BINDING SITE FOR RESIDUE BGC A 99
2AC2SOFTWAREARG A:34 , GLU A:56 , ARG A:67 , ARG A:71 , HIS A:86 , TYR A:87 , HOH A:158 , ARG C:45BINDING SITE FOR RESIDUE SO4 A 98
3AC3SOFTWARESER A:15 , GLU B:43 , ARG B:45 , HOH B:218 , HOH B:255BINDING SITE FOR RESIDUE SO4 B 100
4AC4SOFTWAREARG A:42 , ARG C:34 , GLU C:56 , ARG C:67 , ARG C:71 , HIS C:86 , TYR C:87 , HOH C:234BINDING SITE FOR RESIDUE SO4 C 198
5AC5SOFTWAREARG B:34 , VAL B:38 , PHE B:39 , GLU B:40 , ASN B:41 , ARG B:42 , GLU B:43 , GLU B:56 , ARG B:67 , ARG B:71 , HIS B:86 , TYR B:87BINDING SITE FOR RESIDUE 2GP B 98

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:9 -A:97
2B:9 -B:97
3C:9 -C:97

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:28 -Pro A:29
2Gly B:28 -Pro B:29
3Gly C:28 -Pro C:29
4Pro C:62 -Gly C:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DGY)

(-) 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:92
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:94
                                    79        89        99       109       119       129       139       149       159    
         Q53752_STRAU    70 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3dgya_ A: automated matches                                                                   SCOP domains
               CATH domains 3dgyA00 A:4-97  [code=3.10.450.30, no name defined]                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhhhhh.........eee..............eeeee.....--.....eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 3dgy A   4 ALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPG--DRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    13        23        33        43        53        63  |     73        83        93    
                                                                                      63 66                               


Chain B from PDB  Type:PROTEIN  Length:94
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:97
                                    76        86        96       106       116       126       136       146       156       
         Q53752_STRAU    67 ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3dgyb_ B: automated matches                                                                      SCOP domains
               CATH domains 3dgyB00 B:1-97  [code=3.10.450.30, no name defined]                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.hhhhhhhhhhhhhhhhh...........................eeee....---.....eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3dgy B   1 ADPALADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTP---DRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    10        20        30        40        50        60 |   |  70        80        90       
                                                                                        62  66                               


Chain C from PDB  Type:PROTEIN  Length:91
 aligned with Q53752_STRAU | Q53752 from UniProtKB/TrEMBL  Length:163

    Alignment length:93
                                    80        90       100       110       120       130       140       150       160   
         Q53752_STRAU    71 LADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGSNDRGTRRVVTGGYGEQYWSPDHYATFQEIDPRC 163
               SCOP domains d3dgyc_ C: automated matches                                                                  SCOP domains
               CATH domains 3dgyC00 C:5-97  [code=3.10.450.30, no name defined]                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhh..........eee..............eeeee......--....eeee.....eeee.......eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3dgy C   5 LADVCRTKLPSQAQDTLALIAKNGPYPYNRDGVVFENRESRLPKKGNGYYHEFTVVTPGS--RGTRRVVTGGYGEQYWSPDHYATFQEIDPRC  97
                                    14        24        34        44        54        64  |     74        84        94   
                                                                                      64 67
   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, 3)

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

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q53752_STRAU | Q53752)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid 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:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.

 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
    2GP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BGC  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:28 - Pro A:29   [ RasMol ]  
    Gly B:28 - Pro B:29   [ RasMol ]  
    Gly C:28 - Pro C:29   [ RasMol ]  
    Pro C:62 - Gly C:63   [ 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
  3dgy
    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
  Q53752_STRAU | Q53752
    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)
  3.1.4.8
    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
  Q53752_STRAU | Q53752
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q53752_STRAU | Q53752: 1py3 1pyl 3d4a 3d5g 3d5i 3dh2

(-) Related Entries Specified in the PDB File

1gmp STRUCTURE OF RIBONUCLEASE SA WITH 2'-GMP
1py3 STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND
1pyl STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND
2sar STRUCTURE OF RIBONUCLEASE SA WITH 3'-GMP
3d4a STRUCTURE OF RIBONUCLEASE SA2 WITH 3'-GMP
3d5i CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH EXO-2',3'- CYCLOPHOSPHOROTIOATE
3dh2