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(-) Description

Title :  CRYSTAL STRUCTURE OF PF10_0086, ADENYLATE KINASE FROM PLASMODIUM FALCIPARUM
 
Authors :  A. K. Wernimont, P. Loppnau, L. Crombet, J. Weadge, A. Perieteanu, A. M. C. H. Arrowsmith, H. Park, C. Bountra, R. Hui, M. Amani, Structural Ge Consortium (Sgc)
Date :  30 Aug 11  (Deposition) - 26 Oct 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Rossmann Fold, Transferase, Atp Binding, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, P. Loppnau, L. Crombet, J. Weadge, A. Perieteanu, A. M. Edwards, C. H. Arrowsmith, H. Park, C. Bountra, R. Hui, M. Amani
Crystal Structure Of Pf10_0086, Adenylate Kinase From Plasmodium Falciparum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ADENYLATE KINASE 2
    Chains: A, B, C, D
    EC Number: 2.7.4.3
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP1Ligand/IonADENOSINE MONOPHOSPHATE
3ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP1Ligand/IonADENOSINE MONOPHOSPHATE
3ATP-1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP-1Ligand/IonADENOSINE MONOPHOSPHATE
3ATP-1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP-1Ligand/IonADENOSINE MONOPHOSPHATE
3ATP-1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP-1Ligand/IonADENOSINE MONOPHOSPHATE
3ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:37 , GLY B:38 , SER B:39 , GLY B:40 , LYS B:41 , GLY B:42 , THR B:43 , ARG B:151 , ARG B:155 , ILE B:164 , TYR B:165 , HIS B:166 , PHE B:169 , GLN B:227 , PRO B:228 , ALA B:229 , ADP B:244BINDING SITE FOR RESIDUE ADP B 243
2AC2SOFTWAREGLN A:187 , ARG A:188 , GLU A:189BINDING SITE FOR RESIDUE MG A 243
3AC3SOFTWAREHIS A:239 , GLY A:242 , GLN B:132BINDING SITE FOR RESIDUE MG A 244
4AC4SOFTWAREGLY D:42 , THR D:43 , ARG D:151 , ARG D:155 , GLN D:227 , PRO D:228 , ALA D:229BINDING SITE FOR RESIDUE ATP D 243
5AC5SOFTWAREPRO B:37 , SER B:58 , THR B:59 , GLY B:60 , LEU B:63 , ARG B:64 , ILE B:81 , LYS B:85 , LEU B:86 , VAL B:87 , ASP B:112 , GLY B:113 , TYR B:114 , ARG B:116 , GLN B:120 , ARG B:155 , ARG B:188 , ASP B:190 , ARG B:199 , ADP B:243BINDING SITE FOR RESIDUE ADP B 244
6AC6SOFTWARETHR A:59 , GLY A:60 , LEU A:63 , ILE A:81 , LYS A:85 , LEU A:86 , VAL A:87 , VAL A:92 , GLY A:113 , TYR A:114 , GLN A:120 , ARG A:199BINDING SITE FOR RESIDUE AMP A 245
7AC7SOFTWAREALA A:36 , GLY A:38 , SER A:39 , GLY A:40 , LYS A:41 , GLY A:42 , THR A:43 , ARG A:151 , ARG A:155 , ILE A:164 , TYR A:165 , HIS A:166 , PHE A:169 , GLN A:227 , ALA A:229BINDING SITE FOR RESIDUE ADP A 246

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TLX)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:114 -Pro A:115
2Tyr B:114 -Pro B:115
3Tyr D:114 -Pro D:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TLX)

(-) 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:235
 aligned with Q7Z0H0_PLAFA | Q7Z0H0 from UniProtKB/TrEMBL  Length:242

    Alignment length:235
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237     
         Q7Z0H0_PLAFA     8 FSTIDLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTGDLLREAAEKKTELGLKIKNIINEGKLVDDQMVLSLVDEKLKTPQCKKGFILDGYPRNVKQAEDLNKLLQKNQTKLDGVFYFNVPDEVLVNRISGRLIHKPSGRIYHKIFNPPKVPFRDDVTNEPLIQREDDNEDVLKKRLTVFKSETSPLISYYKNKNLLINLDATQPANDLEKKISQHIDG 242
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------d3tlxa1 A:161-188           ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhheeee....eeee.....................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..eeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tlx A   8 FSTIDLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTGDLLREAAEKKTELGLKIKNIINEGKLVDDQMVLSLVDEKLKTPQCKKGFILDGYPRNVKQAEDLNKLLQKNQTKLDGVFYFNVPDEVLVNRISGRLIHKPSGRIYHKIFNPPKVPFRDDVTNEPLIQREDDNEDVLKKRLTVFKSETSPLISYYKNKNLLINLDATQPANDLEKKISQHIDG 242
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237     


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with Q7Z0H0_PLAFA | Q7Z0H0 from UniProtKB/TrEMBL  Length:242

    Alignment length:240
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242
         Q7Z0H0_PLAFA     3 ENLENFSTIDLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTGDLLREAAEKKTELGLKIKNIINEGKLVDDQMVLSLVDEKLKTPQCKKGFILDGYPRNVKQAEDLNKLLQKNQTKLDGVFYFNVPDEVLVNRISGRLIHKPSGRIYHKIFNPPKVPFRDDVTNEPLIQREDDNEDVLKKRLTVFKSETSPLISYYKNKNLLINLDATQPANDLEKKISQHIDG 242
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhheeee....eeee.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tlx B   3 ENLENFSTIDLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTGDLLREAAEKKTELGLKIKNIINEGKLVDDQMVLSLVDEKLKTPQCKKGFILDGYPRNVKQAEDLNKLLQKNQTKLDGVFYFNVPDEVLVNRISGRLIHKPSGRIYHKIFNPPKVPFRDDVTNEPLIQREDDNEDVLKKRLTVFKSETSPLISYYKNKNLLINLDATQPANDLEKKISQHIDG 242
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242


Chain C from PDB  Type:PROTEIN  Length:155
 aligned with Q7Z0H0_PLAFA | Q7Z0H0 from UniProtKB/TrEMBL  Length:242

    Alignment length:239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
         Q7Z0H0_PLAFA     3 ENLENFSTIDLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTGDLLREAAEKKTELGLKIKNIINEGKLVDDQMVLSLVDEKLKTPQCKKGFILDGYPRNVKQAEDLNKLLQKNQTKLDGVFYFNVPDEVLVNRISGRLIHKPSGRIYHKIFNPPKVPFRDDVTNEPLIQREDDNEDVLKKRLTVFKSETSPLISYYKNKNLLINLDATQPANDLEKKISQHID 241
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh....eee.----.hhhhhhhhhhhhhhheeee.-------------------------------...hhhhhh...---...eeee..---.hhhhhhhhhhhhhh.....eee..------.hhhhhh-------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tlx C   3 ENLENFSTIDLLNELKRRYACLSKPDGRYIF----GSGKGTQSLNLKKSHCYCHLS-------------------------------QMVLSLVDEKLK---CKKGFILDG---NVKQAEDLNKLLQKNQTKLDGVFYF------LVNRISG-------------------------------------NEDVLKKRLTVFKSETSPLISYYKNKNLLINLDATQPANDLEKKISQHID 241
                                    12        22        32|    |  42        52     |   -         -         -       |92        |-  |    112|   |  122       132        |-     | 152 |       -         -         -       192       202       212       222       232         
                                                         33   38                  58                              90        101 105     113 117                     141    148   154                                   192                                                 


Chain D from PDB  Type:PROTEIN  Length:182
 aligned with Q7Z0H0_PLAFA | Q7Z0H0 from UniProtKB/TrEMBL  Length:242

    Alignment length:237
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       
         Q7Z0H0_PLAFA     6 ENFSTIDLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTGDLLREAAEKKTELGLKIKNIINEGKLVDDQMVLSLVDEKLKTPQCKKGFILDGYPRNVKQAEDLNKLLQKNQTKLDGVFYFNVPDEVLVNRISGRLIHKPSGRIYHKIFNPPKVPFRDDVTNEPLIQREDDNEDVLKKRLTVFKSETSPLISYYKNKNLLINLDATQPANDLEKKISQHIDG 242
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....eeeee.------.hhhhhhhhhhh.eeee....-----------.hhhhhhhhh....hhhhhhhhh------hhhhh.eeee....hhhhhhhhhhhhhhh-....eeeeee.hhhhhhhhhhh........-------------------------------.hhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tlx D   6 ENFSTIDLLNELKRRYACLSKPDGRYIFLG------GTQSLNLKKSHCYCHLSTGDL-----------GLKIKNIINEGKLVDDQMVLSLV------PQCKKGFILDGYPRNVKQAEDLNKLLQKN-TKLDGVFYFNVPDEVLVNRISGRLIHKPSG-------------------------------DVLKKRLTVFKSETSPLISYYKNKNLLINLDATQPANDLEKKISQHIDG 242
                                    15        25        35      | 45        55      |  -        75        85        95|      105       115       125     | 135       145       155      |  -         -         -       195       205       215       225       235       
                                                        35     42                  62          74                    96    103                         131 |                          162                             194                                                
                                                                                                                                                         133
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q7Z0H0_PLAFA | Q7Z0H0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004017    adenylate kinase activity    Catalysis of the reaction: ATP + AMP = 2 ADP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0019205    nucleobase-containing compound kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016776    phosphotransferase activity, phosphate group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a phosphate group (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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