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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF DOUBLE-DOMAIN ARGININE KINASE FROM ANTHOPLEURA JAPONICAS IN COMPLEX WITH L-ARGININE AND ATPGS
 
Authors :  Z. Wang, Z. Qiao, S. Ye, R. Zhang
Date :  25 Sep 14  (Deposition) - 08 Apr 15  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Double Domain, Tandem Domain, Phosphagen Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Wang, Z. Qiao, S. Ye, R. Zhang
Structure Of A Double-Domain Phosphagen Kinase Reveals An Asymmetric Arrangement Of The Tandem Domains.
Acta Crystallogr. , Sect. D V. 71 779 2015
PubMed-ID: 25849389  |  Reference-DOI: 10.1107/S1399004715001169

(-) Compounds

Molecule 1 - ARGININE KINASE
    Chains: A, B
    EC Number: 2.7.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: SEA ANEMONE
    Organism Scientific: ANTHOPLEURA JAPONICA
    Organism Taxid: 67755
    Synonym: AK

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2AGS1Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3ARG2Mod. Amino AcidARGININE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2AGS-1Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3ARG1Mod. Amino AcidARGININE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2AGS1Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3ARG1Mod. Amino AcidARGININE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:610 , PHE A:615 , HIS A:617 , THR A:618 , ASP A:619 , TYR A:623BINDING SITE FOR RESIDUE ARG A 801
2AC2SOFTWARESER B:126 , ARG B:128 , ARG B:130 , ARG B:233 , ARG B:284 , SER B:286 , HIS B:288 , ARG B:802BINDING SITE FOR RESIDUE AGS B 801
3AC3SOFTWAREGLY B:68 , VAL B:69 , GLY B:70 , TYR B:72 , PHE B:198 , GLU B:229 , SER B:277 , ASN B:278 , AGS B:801 , HOH B:7197 , HOH B:7266 , HOH B:7360BINDING SITE FOR RESIDUE ARG B 802
4AC4SOFTWAREARG B:128 , HIS B:189BINDING SITE FOR RESIDUE ACT B 803
5AC5SOFTWAREASP B:258 , PHE B:263 , TYR B:271BINDING SITE FOR RESIDUE ACT B 804

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RF9)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser A:95 -Pro A:96
2Trp A:208 -Pro A:209
3Ser A:447 -Pro A:448
4Trp A:560 -Pro A:561
5Ser B:95 -Pro B:96
6Trp B:208 -Pro B:209
7Ser B:447 -Pro B:448
8Trp B:560 -Pro B:561

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RF9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RF9)

(-) Exons   (0, 0)

(no "Exon" information available for 4RF9)

(-) 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:691
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.............hhhhh...........eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh.......hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..ee...ee...hhhhh...eeeeeeeehhhhhhh.hhhhhhhhh.eeeee.....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...hhhhh.....hhhhh...........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh.......hhhhhhhh.........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...ee...ee...hhhhh...eeeeeeee........hhhhhhh...eeee..eeeeee......hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rf9 A   1 MADPETAAKFKSKNAFPDPLNDPKCNPKSLVKKYLTPKVFESLKNKKTKLGITLWDCINSGVVNLDSGVGVYAGDEESYTLFGPLFDAIIEDYHSPYKLATGHNSDMNPAHVKAPDLDPANRYIRSTRIRVARSLKGYGLAPGVTKAHRLEIEKKVVGVLTSLTGDLAGKYYPLSGMDEKTRQQLVDDHFLFKKGDRFLEAAGINKEWPEGRGIYHNNDKTFLVWLNEEDHLRIISMEKGSDIGSVFSRLCRAVNEIDKKLGFQHTKKHGYLTSCPSNLGTGMRASVHVKIPHAKEHPDFENILTKYHIQARGIEDAGVYDISNRRRLGLSEVQCVQDMYDGVKALMELEKEAIAKKRSVFPEVLKNPEVKSLLRKYLTPELFDSLKDKKTAKGISLYDCINSGVENLDSSCGVYAGDEECYTLFAPLFDKIVEDYHSPYKLANKHTSDMNPEKVDAPNLDPEGTYIRSTRIRVARNVKGYALTPGLTRNERLDIERKVVGVLSSLTGDLAGQYYPLTGMDEATRQKLVNDHFLFKKGDRFLEAAGVNKLWPEGRGIFHNNDKTFLVWINEEDQLRIISMEKGSDIGSVFGRLCRAVNEIDKQLGFQHTDAHGYLSGCPTNLGTGMRASVHVKIPKASAHPDFQKICDEFHIQARGGVFDISNRRRLGLSEVQCVQDMYNGVKKLLEIEKR 801
                                    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   ||  329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659     ||682       692       702       712|
                                                                                                                                                                                                                                                                                                                                                   314|                                                                                                                                                                                                                                                                                                                                                  665|                              712|
                                                                                                                                                                                                                                                                                                                                                    324                                                                                                                                                                                                                                                                                                                                                   679                               801


Chain B from PDB  Type:PROTEIN  Length:687
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.............hhhhh...........eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh.......hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..ee...ee...hhhhh...eeeeeeee..hhhhh.hhhhhhhhh.eeee......eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhh..........hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.............hhhhh...........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhh........hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...ee...ee...hhhhh...eeeeeee..........hhhhhhhh.ee...eee......hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rf9 B   1 MADPETAAKFKSKNAFPDPLNDPKCNPKSLVKKYLTPKVFESLKNKKTKLGITLWDCINSGVVNLDSGVGVYAGDEESYTLFGPLFDAIIEDYHSPYKLATGHNSDMNPAHVKAPDLDPANRYIRSTRIRVARSLKGYGLAPGVTKAHRLEIEKKVVGVLTSLTGDLAGKYYPLSGMDEKTRQQLVDDHFLFKKGDRFLEAAGINKEWPEGRGIYHNNDKTFLVWLNEEDHLRIISMEKGSDIGSVFSRLCRAVNEIDKKLGFQHTKKHGYLTSCPSNLGTGMRASVHVKIPHAKEHPDFENILTKYHIQARGIEDAGVYDISNRRRLGLSEVQCVQDMYDGVKALMELEKEAIAKKRSVFPEVLKNPEVKSLLRKYLTPELFDSLKDKKTAKGISLYDCINSGVENLDSSCGVYAGDEECYTLFAPLFDKIVEDYHSPYKLANKHTSDMNPEKVDAPNLDPEGTYIRSTRIRVARNVKGYALTPGLTRNERLDIERKVVGVLSSLTGDLAGQYYPLTGMDEATRQKLVNDHFLFKKGDRFLEAAGVNKLWPEGRGIFHNNDKTFLVWINEEDQLRIISMEKGSDIGSVFGRLCRAVNEIDKQLGFQHTDAHGYLSGCPTNLGTGMRASVHVKIPKASAHPDFQKICDEFHIQARDISNRRRLGLSEVQCVQDMYNGVKKLLEIEKR 802
                                    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   ||  329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659    || 686       696       706     ||
                                                                                                                                                                                                                                                                                                                                                   314|                                                                                                                                                                                                                                                                                                                                                 664|                           712|
                                                                                                                                                                                                                                                                                                                                                    324                                                                                                                                                                                                                                                                                                                                                  682                            802
   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 4RF9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RF9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RF9)

(-) Gene Ontology  (8, 8)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AGS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ARG  [ 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
    Ser A:447 - Pro A:448   [ RasMol ]  
    Ser A:95 - Pro A:96   [ RasMol ]  
    Ser B:447 - Pro B:448   [ RasMol ]  
    Ser B:95 - Pro B:96   [ RasMol ]  
    Trp A:208 - Pro A:209   [ RasMol ]  
    Trp A:560 - Pro A:561   [ RasMol ]  
    Trp B:208 - Pro B:209   [ RasMol ]  
    Trp B:560 - Pro B:561   [ RasMol ]  
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  4rf9
    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
  KARG_ANTJA | O15992
    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)
  2.7.3.3
    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
  KARG_ANTJA | O15992
    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
        KARG_ANTJA | O15992: 4rf6 4rf7 4rf8

(-) Related Entries Specified in the PDB File

4rf6 4rf7 4rf8