Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STAPHYLOCOCCAL NUCLEASE DIMER CONTAINING A DELETION OF RESIDUES 114-119 COMPLEXED WITH CALCIUM CHLORIDE AND THE COMPETITIVE INHIBITOR DEOXYTHYMIDINE-3',5'-DIPHOSPHATE
 
Authors :  S. M. Green, A. G. Gittis, A. K. Meeker, E. E. Lattman
Date :  23 Aug 96  (Deposition) - 21 Apr 97  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Hydrolase, Nuclease, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Green, A. G. Gittis, A. K. Meeker, E. E. Lattman
One-Step Evolution Of A Dimer From A Monomeric Protein.
Nat. Struct. Biol. V. 2 746 1995
PubMed-ID: 7552745  |  Reference-DOI: 10.1038/NSB0995-746

(-) Compounds

Molecule 1 - STAPHYLOCOCCAL NUCLEASE DIMER
    Chains: A, B
    EC Number: 3.1.31.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: LAMBDA PL12
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: ALTHOUGH THE LIGANDS WERE ADDED FOR CRYSTALLIZATION, THEY WERE NOT OBSERVED IN THE ELECTRON DENSITY MAPS AND WERE NOT INCLUDED IN THE FINAL STRUCTURE
    Strain: FOGGI

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1SND)

(-) Sites  (0, 0)

(no "Site" information available for 1SND)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SND)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SND)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SND)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNASE_3PS50830 Thermonuclease domain profile.NUC_STAAU90-224
 		  2A:8-141
B:8-141
2TNASE_1PS01123 Thermonuclease family signature 1.NUC_STAAU101-125
 		  2A:19-43
B:19-43
3TNASE_2PS01284 Thermonuclease family signature 2.NUC_STAAU165-175
 		  2A:83-93
B:83-93
Biological Unit 1 (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNASE_3PS50830 Thermonuclease domain profile.NUC_STAAU90-224
 		  4A:8-141
B:8-141
2TNASE_1PS01123 Thermonuclease family signature 1.NUC_STAAU101-125
 		  4A:19-43
B:19-43
3TNASE_2PS01284 Thermonuclease family signature 2.NUC_STAAU165-175
 		  4A:83-93
B:83-93
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNASE_3PS50830 Thermonuclease domain profile.NUC_STAAU90-224
 		  2A:8-141
B:8-141
2TNASE_1PS01123 Thermonuclease family signature 1.NUC_STAAU101-125
 		  2A:19-43
B:19-43
3TNASE_2PS01284 Thermonuclease family signature 2.NUC_STAAU165-175
 		  2A:83-93
B:83-93

(-) Exons   (0, 0)

(no "Exon" information available for 1SND)

(-) 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:129
 aligned with NUC_STAAU | P00644 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:135
                                    98       108       118       128       138       148       158       168       178       188       198       208       218     
            NUC_STAAU    89 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWS 223
               SCOP domains d1snda_ A: Staphylococcal nuclease                                                                                                      SCOP domains
               CATH domains 1sndA00 A:7-141  [code=2.40.50.90, no name defined]                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eeeeee..eeeeeee..................hhhhhhhhhhhhh....eeee............eeeeeee....hhhhhhh........------..hhhhhhhhhhhhh...hhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TNASE_3  PDB: A:8-141 UniProt: 90-224                                                                                                  PROSITE (1)
                PROSITE (2) ------------TNASE_1  PDB: A:19-43    ---------------------------------------TNASE_2    ------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1snd A   7 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAY------THEQHLRKSEAQAKKEKLNIWS 141
                                    16        26        36        46        56        66        76        86        96       106      |  -   |   126       136     
                                                                                                                                    113    120                     


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with NUC_STAAU | P00644 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:135
                                    98       108       118       128       138       148       158       168       178       188       198       208       218     
            NUC_STAAU    89 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWS 223
               SCOP domains d1sndb_ B: Staphylococcal nuclease                                                                                                      SCOP domains
               CATH domains 1sndB00 B:7-141  [code=2.40.50.90, no name defined]                                                                                     CATH domains
           Pfam domains (1) --------------------------SNase-1sndB01 B:33-141                                                                                        Pfam domains (1)
           Pfam domains (2) --------------------------SNase-1sndB02 B:33-141                                                                                        Pfam domains (2)
         Sec.struct. author ...eeeeeeee....eeeeee..eeeeeee..................hhhhhhhhhhhhh....eeee............eeeeeee....hhhhhhhh.......------..hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TNASE_3  PDB: B:8-141 UniProt: 90-224                                                                                                  PROSITE (1)
                PROSITE (2) ------------TNASE_1  PDB: B:19-43    ---------------------------------------TNASE_2    ------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1snd B   7 LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAY------THEQHLRKSEAQAKKEKLNIWS 141
                                    16        26        36        46        56        66        76        86        96       106      |  -   |   126       136     
                                                                                                                                    113    120
   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: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: SNase] (72)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NUC_STAAU | P00644)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
(no "Ligands, Modified Residues, Ions" information available for 1snd)
 
  Sites
(no "Sites" information available for 1snd)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1snd)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 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
  1snd
    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
  NUC_STAAU | P00644
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.31.1
    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
  NUC_STAAU | P00644
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NUC_STAAU | P00644: 1a2t 1a2u 1a3t 1a3u 1a3v 1aex 1ena 1enc 1eqv 1ey0 1ey4 1ey5 1ey6 1ey7 1ey8 1ey9 1eya 1eyc 1eyd 1ez6 1ez8 1f2m 1f2y 1f2z 1ihz 1ii3 1jok 1joo 1joq 1jor 1kaa 1kab 1kda 1kdb 1kdc 1nsn 1nuc 1rkn 1snc 1snm 1sno 1snp 1snq 1sta 1stb 1stg 1sth 1stn 1sty 1syb 1syc 1syd 1sye 1syf 1syg 1tqo 1tr5 1tt2 1u9r 2enb 2exz 2ey1 2ey2 2ey5 2ey6 2eyf 2eyh 2eyj 2eyl 2eym 2eyo 2eyp 2f0d 2f0e 2f0f 2f0g 2f0h 2f0i 2f0j 2f0k 2f0l 2f0m 2f0n 2f0o 2f0p 2f0q 2f0s 2f0t 2f0u 2f0v 2f0w 2f3v 2f3w 2fxy 2fxz 2gsi 2khs 2nuc 2oeo 2of1 2pqe 2qdb 2rbm 2rdf 2rks 2snm 2sns 2sob 3bdc 3c1e 3c1f 3d4d 3d6c 3dhq 3dmu 3e5s 3eji 3ero 3erq 3evq 3h6m 3hej 3hzx 3itp 3lx0 3meh 3mhb 3mvv 3mxp 3mz5 3nhh 3nk9 3np8 3nqt 3nuc 3nxw 3oso 3owf 3p1h 3p75 3pmf 3qb3 3qoj 3qol 3qon 3r3o 3ruz 3s9w 3shl 3sk4 3sk5 3sk6 3sk8 3sr1 3sxh 3t13 3t16 3tme 3tp5 3tp6 3tp7 3tp8 3u9o 3v2t 3va5 4df7 4dfa 4dgz 4du9 4e6i 4eqn 4eqo 4eqp 4evo 4f7x 4f8m 4g57 4h7b 4hmi 4hmj 4hth 4i65 4ial 4id6 4iun 4iz8 4j1m 4j6h 4k14 4k2k 4k2l 4k5v 4k5w 4k5x 4k6d 4k8i 4k8j 4kd3 4kd4 4khv 4kjn 4kjo 4kta 4kv6 4ky5 4ky6 4ky7 4laa 4me5 4miu 4n9p 4n9t 4ndx 4nkl 4nmz 4np5 4odg 4ol7 4pmb 4pmc 4pny 4qb4 4qf4 4r8n 4rkb 4rkl 4s3s 4trd 4wor 4yij 4zq3 4zui 4zuj 5c3w 5c3x 5c4h 5c4z 5c5l 5c5m 5c6a 5cc4 5cgk 5cr3 5cv4 5cv5 5cv6 5cv7 5cv8 5cv9 5dau 5deh 5e1f 5e3f 5egt 5ekk 5ekl 5f2d 5hgt 5hur 5i6w 5i6y 5i9o 5i9p 5igb 5igc 5igd 5ige 5igf 5igg 5iif 5ioc 5iod 5isr 5j1z 5j22 5jav 5job 5k5p 5kee 5kgu 5kix 5kru 5kyi 5kyl 5nuc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SND)