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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ADENYLATE KINASE MUTANT--AKM1
 
Authors :  S. Moon, E. Bae
Date :  09 Jul 14  (Deposition) - 26 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Adenylate Kinase, Atp Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Moon, E. Bae
Crystal Structures Of Thermally Stable Adenylate Kinase Mutants Designed By Local Structural Entropy Optimization And Structure-Guided Mutagenesis
J Korean Soc Appl Biol Chem V. 57 661 2014
PubMed: search  |  Reference-DOI: 10.1007/S13765-014-4228-4

(-) Compounds

Molecule 1 - ADENYLATE KINASE
    Chains: C, B, A, D
    EC Number: 2.7.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ADK, BSU01370
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS 168
    Organism Taxid: 224308

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1AP54Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AP51Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AP51Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1AP51Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1AP51Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO C:9 , GLY C:10 , GLY C:12 , LYS C:13 , GLY C:14 , THR C:15 , THR C:31 , ARG C:36 , ILE C:53 , GLU C:57 , LEU C:58 , VAL C:59 , THR C:64 , GLY C:85 , ARG C:88 , GLN C:92 , ARG C:123 , LEU C:124 , ARG C:127 , TYR C:137 , HIS C:138 , ARG C:160 , ARG C:171 , GLY C:197 , GLN C:199 , ASP C:200 , MET C:201 , VAL C:204 , HOH C:405binding site for residue AP5 C 301
2AC2SOFTWARECYS B:130 , CYS B:133 , CYS B:150 , ASP B:153binding site for residue ZN B 301
3AC3SOFTWAREPRO B:9 , GLY B:10 , ALA B:11 , GLY B:12 , LYS B:13 , GLY B:14 , THR B:15 , THR B:31 , GLY B:32 , ARG B:36 , GLU B:57 , LEU B:58 , VAL B:59 , THR B:64 , GLY B:85 , ARG B:88 , GLN B:92 , ARG B:127 , THR B:136 , TYR B:137 , HIS B:138 , ARG B:160 , ARG B:171 , GLN B:199 , MET B:201binding site for residue AP5 B 302
4AC4SOFTWARECYS A:130 , CYS A:133 , CYS A:150 , ASP A:153binding site for residue ZN A 301
5AC5SOFTWAREPRO A:9 , GLY A:10 , ALA A:11 , GLY A:12 , LYS A:13 , GLY A:14 , THR A:15 , THR A:31 , GLY A:32 , PHE A:35 , ARG A:36 , GLU A:57 , VAL A:59 , THR A:64 , GLY A:85 , PHE A:86 , ARG A:88 , GLN A:92 , ARG A:123 , LEU A:124 , ARG A:127 , HIS A:138 , ARG A:160 , ARG A:171 , GLN A:199 , MET A:201binding site for residue AP5 A 302
6AC6SOFTWAREPRO D:9 , GLY D:10 , ALA D:11 , GLY D:12 , LYS D:13 , GLY D:14 , THR D:15 , THR D:31 , GLY D:32 , PHE D:35 , ARG D:36 , GLU D:57 , VAL D:59 , THR D:64 , GLY D:85 , PHE D:86 , ARG D:88 , GLN D:92 , ARG D:123 , LEU D:124 , ARG D:127 , THR D:136 , TYR D:137 , HIS D:138 , PHE D:141 , ARG D:160 , ARG D:171 , GLY D:197 , GLN D:199binding site for residue AP5 D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe C:86 -Pro C:87
2Phe B:86 -Pro B:87
3Phe A:86 -Pro A:87
4Phe D:86 -Pro D:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TYP)

(-) 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh.eee.....ee...................ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4typ A   1 MNIVLMGLPGAGKGTQAEKIVAKYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVRERLSRGFLLDGFPRTVAQAEALEEILEEMGRKLEHVIHIDVRQEELMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVAKRLEVNMKQMKPLLAFYDSKEVLRNVNGEQDMEKVFKDLRELLQ 213
                                    10        20        30        40        50        60        70  ||    85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                                                                   73|                                                                                                                                      
                                                                                                    79                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhheeee.....eee..................ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4typ B   1 MNIVLMGLPGAGKGTQAEKIVAKYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVRERLSGFLLDGFPRTVAQAEALEEILEEMGRKLEHVIHIDVRQEELMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVAKRLEVNMKQMKPLLAFYDSKEVLRNVNGEQDMEKVFKDLRELL 212
                                    10        20        30        40        50        60        70  ||    86        96       106       116       126       136       146       156       166       176       186       196       206      
                                                                                                   73|                                                                                                                                    
                                                                                                    80                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhee..ee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4typ C   1 MNIVLMGLPGAGKGTQAEKIVAKYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVRERLSGFLLDGFPRTVAQAEALEEILEEMGRKLEHVIHIDVRQEELMERLTGRRITYHLVFNPPKTPYQRADDNEETVAKRLEVNMKQMKPLLAFYDSKEVLRNVNGEQDMEKVFKDLRELL 212
                                    10        20        30        40        50        60        70  ||    86        96       106       116       126  ||   142    || 162       172       182       192       202       212
                                                                                                   73|                                              129|        147|                                                      
                                                                                                    80                                               136         158                                                      


Chain D from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhh...eeehhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhee..ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4typ D   1 MNIVLMGLPGAGKGTQAEKIVAKYGIPHISTGDMFRAAMKEAKSYIDKGELVPDEVTIGIVRERLSGFLLDGFPRTVAQAEALEEILEEMGRKLEHVIHIDVRQEELMERLTGRRITYHLVFNPPKTPLYQRADDNEETVAKRLEVNMKQMKPLLAFYDSKEVLRNVNGEQDMEKVFKDLRELLQG 214
                                    10        20        30        40||      57        67     || 83        93       103       113       123     ||139       158       168       178       188       198       208      
                                                                   41|                      73|                                              129|        147|                                                         
                                                                    49                       80                                               136         157
   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 4TYP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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        KAD_BACSU | P16304: 1p3j 2eu8 2oo7 2ori 2osb 2p3s 2qaj 3dkv 3dl0 4mkf 4mkg 4mkh 4qbf 4qbg 4tyq

(-) Related Entries Specified in the PDB File

4mkg 4tyq