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(-) Description

Title :  CRYSTAL STRUCTURE OF DOUBLE-DOMAIN ARGININE KINASE FROM ANTHOPLEURA JAPONICAS IN COMPLEX WITH ADP
 
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 :  2.17
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Double Domain, Tandem Domain, Phsphagen 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
    ChainsA, B
    EC Number2.7.3.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonSEA ANEMONE
    Organism ScientificANTHOPLEURA JAPONICA
    Organism Taxid67755
    SynonymAK

 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, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NO320Ligand/IonNITRATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NO39Ligand/IonNITRATE ION
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NO311Ligand/IonNITRATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:126 , ARG A:128 , ARG A:130 , ARG A:284 , SER A:286 , VAL A:287 , HIS A:288 , ASP A:330 , HOH A:1236BINDING SITE FOR RESIDUE ADP A 1001
02AC2SOFTWAREASP A:610 , PHE A:615 , TYR A:623BINDING SITE FOR RESIDUE NO3 A 1002
03AC3SOFTWAREASP A:258 , PHE A:263 , TYR A:271BINDING SITE FOR RESIDUE NO3 A 1003
04AC4SOFTWAREASP A:458 , LYS A:463 , SER A:692 , VAL A:694 , ASN B:453BINDING SITE FOR RESIDUE NO3 A 1004
05AC5SOFTWARELEU A:65 , ASP A:66BINDING SITE FOR RESIDUE NO3 A 1005
06AC6SOFTWARETYR A:171BINDING SITE FOR RESIDUE NO3 A 1006
07AC7SOFTWAREGLY A:68 , VAL A:69 , TYR A:72 , HOH A:1119 , HOH A:1273BINDING SITE FOR RESIDUE NO3 A 1007
08AC8SOFTWARELYS A:454 , HIS A:455 , THR A:456 , LYS B:463 , NO3 B:804 , NO3 B:806BINDING SITE FOR RESIDUE NO3 A 1008
09AC9SOFTWAREARG A:480 , ARG A:482 , ARG A:585BINDING SITE FOR RESIDUE NO3 A 1009
10BC1SOFTWAREGLU A:153 , GLY A:211 , LYS B:47BINDING SITE FOR RESIDUE NO3 A 1010
11BC2SOFTWARETHR A:456 , GLN A:695 , THR B:456 , GLY B:690 , GLN B:695 , NO3 B:804 , HOH B:901BINDING SITE FOR RESIDUE NO3 B 801
12BC3SOFTWARESER B:126 , ARG B:128 , ARG B:130 , ARG B:284 , SER B:286 , VAL B:287 , HIS B:288 , ASP B:330 , HOH B:1104BINDING SITE FOR RESIDUE ADP B 802
13BC4SOFTWAREASP B:610 , PHE B:615 , TYR B:623 , NO3 B:807BINDING SITE FOR RESIDUE NO3 B 803
14BC5SOFTWAREASN A:453 , THR A:456 , NO3 A:1008 , ASP B:458 , LYS B:463 , SER B:692 , NO3 B:801BINDING SITE FOR RESIDUE NO3 B 804
15BC6SOFTWAREHIS B:446 , ARG B:687 , ARG B:688 , LEU B:689 , HOH B:1118BINDING SITE FOR RESIDUE NO3 B 805
16BC7SOFTWARENO3 A:1008 , SER B:457BINDING SITE FOR RESIDUE NO3 B 806
17BC8SOFTWARESER B:457 , MET B:459 , ASP B:610 , TYR B:623 , NO3 B:803BINDING SITE FOR RESIDUE NO3 B 807
18BC9SOFTWAREGLU B:91 , HOH B:1020BINDING SITE FOR RESIDUE NO3 B 808
19CC1SOFTWAREARG B:122 , ILE B:404 , PRO B:494 , GLY B:495 , LYS B:558BINDING SITE FOR RESIDUE NO3 B 809
20CC2SOFTWAREASN B:121 , TYR B:123 , ARG B:125 , HOH B:1191BINDING SITE FOR RESIDUE NO3 B 810
21CC3SOFTWARELEU B:150 , GLU B:153 , SER B:175 , GLY B:211BINDING SITE FOR RESIDUE NO3 B 811
22CC4SOFTWAREGLY B:68 , VAL B:69 , GLY B:70 , TYR B:72BINDING SITE FOR RESIDUE NO3 B 812
23CC5SOFTWAREGLN A:695 , ASP A:699 , TYR B:449 , ASN B:453 , ARG B:687 , GLY B:690 , GLN B:695 , ASP B:699 , HOH B:925BINDING SITE FOR RESIDUE EPE B 813
24CC6SOFTWAREPRO B:461 , GLU B:462 , VAL B:464 , ALA B:466 , ASP B:594 , GLY B:596 , SER B:597BINDING SITE FOR RESIDUE EPE B 814

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RF8)

(-) 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 4RF8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RF8)

(-) Exons   (0, 0)

(no "Exon" information available for 4RF8)

(-) 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:686
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.............hhhhh...........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh.......hhhhhh...........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...ee...ee...hhhhh...eeeeeeeehhhhhhh.hhhhhhhhhheeeee....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...hhhhh.....hhhhh...........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh.......hhhhhhhh.........eeeee....eeeee.....eeeeeee...hhhhhhhhhhhhhhhhhhhh...ee...ee...hhhhh...eeeeeee...hhhhh.hhhhhhhhhheeee..eeee......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rf8 A   3 DPETAAKFKSKNAFPDPLNDPKCNPKSLVKKYLTPKVFESLKNKKTKLGITLWDCINSGVVNLDSGVGVYAGDEESYTLFGPLFDAIIEDYHSPYKLATGHNSDMNPAHVKAPDLDPANRYIRSTRIRVARSLKGYGLAPGVTKAHRLEIEKKVVGVLTSLTGDLAGKYYPLSGMDEKTRQQLVDDHFLFKKGDRFLEAAGINKEWPEGRGIYHNNDKTFLVWLNEEDHLRIISMEKGSDIGSVFSRLCRAVNEIDKKLGFQHTKKHGYLTSCPSNLGTGMRASVHVKIPHAKEHPDFENILTKYHIQARGIDAGVYDISNRRRLGLSEVQCVQDMYDGVKALMELEKEAIAKKRSVFPEVLKNPEVKSLLRKYLTPELFDSLKDKKTAKGISLYDCINSGVENLDSSCGVYAGDEECYTLFAPLFDKIVEDYHSPYKLANKHTSDMNPEKVDAPNLDPEGTYIRSTRIRVARNVKGYALTPGLTRNERLDIERKVVGVLSSLTGDLAGQYYPLTGMDEATRQKLVNDHFLFKKGDRFLEAAGVNKLWPEGRGIFHNNDKTFLVWINEEDQLRIISMEKGSDIGSVFGRLCRAVNEIDKQLGFQHTDAHGYLSGCPTNLGTGMRASVHVKIPKASAHPDFQKICDEFHIQARGFDISNRRRLGLSEVQCVQDMYNGVKKLLEIEKS 713
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312 ||    332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662  ||   687       697       707      
                                                                                                                                                                                                                                                                                                                                                 314|                                                                                                                                                                                                                                                                                                                                                 665|                                
                                                                                                                                                                                                                                                                                                                                                  325                                                                                                                                                                                                                                                                                                                                                  681                                

Chain B from PDB  Type:PROTEIN  Length:693
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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..hhhhhhhhhhhhhhhhhhhh...ee...ee...hhhhh...eeeeeeee..hhhhh.hhhhhhhhh.eeeee....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...hhhhh.....hhhhh...........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh.......hhhhhh...........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..ee...ee...hhhhh...eeeeeeee..hhhhh.hhhhhhhhh.eeee......eeeeee......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rf8 B   2 ADPETAAKFKSKNAFPDPLNDPKCNPKSLVKKYLTPKVFESLKNKKTKLGITLWDCINSGVVNLDSGVGVYAGDEESYTLFGPLFDAIIEDYHSPYKLATGHNSDMNPAHVKAPDLDPANRYIRSTRIRVARSLKGYGLAPGVTKAHRLEIEKKVVGVLTSLTGDLAGKYYPLSGMDEKTRQQLVDDHFLFKKGDRFLEAAGINKEWPEGRGIYHNNDKTFLVWLNEEDHLRIISMEKGSDIGSVFSRLCRAVNEIDKKLGFQHTKKHGYLTSCPSNLGTGMRASVHVKIPHAKEHPDFENILTKYHIQARGIDAGVYDISNRRRLGLSEVQCVQDMYDGVKALMELEKEAIAKKRSVFPEVLKNPEVKSLLRKYLTPELFDSLKDKKTAKGISLYDCINSGVENLDSSCGVYAGDEECYTLFAPLFDKIVEDYHSPYKLANKHTSDMNPEKVDAPNLDPEGTYIRSTRIRVARNVKGYALTPGLTRNERLDIERKVVGVLSSLTGDLAGQYYPLTGMDEATRQKLVNDHFLFKKGDRFLEAAGVNKLWPEGRGIFHNNDKTFLVWINEEDQLRIISMEKGSDIGSVFGRLCRAVNEIDKQLGFQHTDAHGYLSGCPTNLGTGMRASVHVKIPKASAHPDFQKICDEFHIQARGIEDAGVFDISNRRRLGLSEVQCVQDMYNGVKKLLEIEKS 713
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  ||   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661    || 680       690       700       710   
                                                                                                                                                                                                                                                                                                                                                  314|                                                                                                                                                                                                                                                                                                                                                  666|                                     
                                                                                                                                                                                                                                                                                                                                                   325                                                                                                                                                                                                                                                                                                                                                   676                                     

   Legend:   → Mismatch (orange background)
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  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 4RF8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RF8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RF8)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KARG_ANTJA | O159924rf6 4rf7 4rf9

(-) Related Entries Specified in the PDB File

4rf6 4rf7 4rf9