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(-) Description

Title :  CRYSTAL STRUCTURE OF A STABLE ADENYLATE KINASE VARIANT AKV3
 
Authors :  S. Moon, D. Jung, E. Bae
Date :  05 Sep 13  (Deposition) - 26 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Adenylate Kinase, Zinc Finger, Transferase Activity, Phosphotransferase Activity, Zinc Binding, Atp Binding, Phosphorylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Moon, D. Jung, G. N. Phillips, E. Bae
An Integrated Approach For Thermal Stabilization Of A Mesophilic Adenylate Kinase
Proteins 2014
PubMed-ID: 24615904  |  Reference-DOI: 10.1002/PROT.24549

(-) Compounds

Molecule 1 - ADENYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ADK, BSU01370
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 224308
    Strain: 168

 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  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1AP52Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2CA7Ligand/IonCALCIUM ION
3MG2Ligand/IonMAGNESIUM ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AP51Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AP51Ligand/IonBIS(ADENOSINE)-5'-PENTAPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:130 , CYS A:133 , CYS A:150 , ASP A:153BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREAP5 A:303 , HOH A:421 , HOH A:445 , HOH A:450 , HOH A:589BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWAREPRO 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 , ILE A:53 , GLU A:57 , VAL A:59 , THR A:64 , GLY A:85 , PHE A:86 , ARG A:88 , GLN A:92 , ARG A:123 , ARG A:127 , THR A:136 , TYR A:137 , HIS A:138 , PHE A:141 , ARG A:160 , ARG A:171 , GLN A:199 , ILE A:201 , MG A:302 , HOH A:416 , HOH A:420 , HOH A:421 , HOH A:434 , HOH A:435 , HOH A:445 , HOH A:449 , HOH A:506 , HOH A:507 , HOH A:589BINDING SITE FOR RESIDUE AP5 A 303
04AC4SOFTWAREGLN A:199 , HOH A:459 , HOH A:585BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREASP A:203 , HOH A:628 , HOH A:629BINDING SITE FOR RESIDUE CA A 305
06AC6SOFTWAREGLY A:73 , HOH A:517 , HOH A:519 , HOH A:591 , HOH A:624BINDING SITE FOR RESIDUE CA A 306
07AC7SOFTWARECYS B:130 , CYS B:133 , CYS B:150 , ASP B:153BINDING SITE FOR RESIDUE ZN B 301
08AC8SOFTWAREAP5 B:303 , HOH B:421 , HOH B:442 , HOH B:443 , HOH B:445BINDING SITE FOR RESIDUE MG B 302
09AC9SOFTWAREPRO 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 , ILE B:53 , GLU B:57 , VAL B:59 , THR B:64 , GLY B:85 , PHE B:86 , ARG B:88 , GLN B:92 , ARG B:123 , LEU B:124 , ARG B:127 , THR B:136 , TYR B:137 , HIS B:138 , PHE B:141 , ARG B:160 , ARG B:171 , GLY B:197 , GLN B:199 , ILE B:201 , MG B:302 , HOH B:407 , HOH B:408 , HOH B:421 , HOH B:423 , HOH B:424 , HOH B:427 , HOH B:442 , HOH B:443 , HOH B:446 , HOH B:471 , HOH B:478BINDING SITE FOR RESIDUE AP5 B 303
10BC1SOFTWAREASP B:200 , HOH B:627 , HOH B:628 , HOH B:629 , HOH B:630 , HOH B:631BINDING SITE FOR RESIDUE CA B 304
11BC2SOFTWAREASP B:200 , HOH B:402 , HOH B:473 , HOH B:588 , HOH B:592 , HOH B:636BINDING SITE FOR RESIDUE CA B 305
12BC3SOFTWAREGLN B:199 , HOH B:587 , HOH B:613 , HOH B:614BINDING SITE FOR RESIDUE CA B 306
13BC4SOFTWAREHOH A:436 , HOH A:617 , LYS B:40 , HOH B:495 , HOH B:586 , HOH B:625 , HOH B:626BINDING SITE FOR RESIDUE CA B 307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:86 -Pro A:87
2Phe B:86 -Pro B:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MKF)

(-) 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:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhheeee.....eee..................ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mkf A   1 MNLVLMGLPGAGKGTQGEKIVEDYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVKERLGKDDCERGFLLDGFPRTVAQAEALEEILEEYGKPIDYVINIEVRKDVLMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVSKRLEVNMKQMQPLLDFYSEKGYLANVNGEQDIEDVYADVKDLLGGLKK 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhheeee.....eee..................ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mkf B   1 MNLVLMGLPGAGKGTQGEKIVEDYGIPHISTGDMFRAAMKEETPLGLEAKSYIDKGELVPDEVTIGIVKERLGKDDCERGFLLDGFPRTVAQAEALEEILEEYGKPIDYVINIEVRKDVLMERLTGRRICSVCGTTYHLVFNPPKTPGICDKDGGELYQRADDNEETVSKRLEVNMKQMQPLLDFYSEKGYLANVNGEQDIEDVYADVKDLLGGLKK 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4MKF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4mkg 4mkh 4qbf 4qbg 4typ 4tyq

(-) Related Entries Specified in the PDB File

4mkg 4mkh