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(-) Description

Title :  CRYSTAL STRUCTURES OF ADENYLATE KINASE WITH 2ADP'S
 
Authors :  Y. -J. Cho, D. Kern
Date :  12 Mar 13  (Deposition) - 25 Jun 14  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Adp Binding, Phosphoryl Transfer Reaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Kerns, R. V. Agafonov, Y. J. Cho, F. Pontiggia, R. Otten, D. V. Pachov, S. Kutter, L. A. Phung, P. N. Murphy, V. Thai, T. Alber, M. F. Hagan, D. Kern
The Energy Landscape Of Adenylate Kinase During Catalysis.
Nat. Struct. Mol. Biol. V. 22 124 2015
PubMed-ID: 25580578  |  Reference-DOI: 10.1038/NSMB.2941

(-) Compounds

Molecule 1 - ADENYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: TRANSFERASE
    Gene: ADK, AQ_078
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: AK, ATP-AMP TRANSPHOSPHORYLASE

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , ALA A:11 , GLY A:12 , LYS A:13 , GLY A:14 , THR A:15 , ARG A:120 , ARG A:124 , TYR A:134 , HIS A:135 , TYR A:138 , LYS A:189 , PRO A:190 , VAL A:191 , ADP A:302 , HOH A:414 , HOH A:458 , HOH A:473 , HOH A:483 , HOH A:492 , HOH A:559 , HOH A:592BINDING SITE FOR RESIDUE ADP A 301
2AC2SOFTWAREPRO A:9 , THR A:31 , GLY A:32 , LEU A:35 , ARG A:36 , MET A:53 , GLU A:57 , VAL A:59 , ILE A:64 , GLY A:82 , ARG A:85 , GLN A:89 , ARG A:124 , ARG A:150 , ARG A:161 , ADP A:301 , HOH A:408 , HOH A:412 , HOH A:415 , HOH A:427 , HOH A:428 , HOH A:445 , HOH A:707BINDING SITE FOR RESIDUE ADP A 302
3AC3SOFTWAREPRO B:9 , THR B:31 , GLY B:32 , LEU B:35 , ARG B:36 , MET B:53 , GLU B:57 , VAL B:59 , ILE B:64 , GLY B:82 , ARG B:85 , GLN B:89 , ARG B:124 , ARG B:150 , ARG B:161 , ADP B:302 , HOH B:404 , HOH B:412 , HOH B:413 , HOH B:414 , HOH B:430 , HOH B:440 , HOH B:554BINDING SITE FOR RESIDUE ADP B 301
4AC4SOFTWAREGLY B:10 , ALA B:11 , GLY B:12 , LYS B:13 , GLY B:14 , THR B:15 , ARG B:120 , ARG B:124 , VAL B:133 , TYR B:134 , HIS B:135 , TYR B:138 , LYS B:189 , PRO B:190 , VAL B:191 , ADP B:301 , HOH B:409 , HOH B:486BINDING SITE FOR RESIDUE ADP B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:83 -Pro A:84
2Phe B:83 -Pro B:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JLB)

(-) 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:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhheee......eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jlb A   1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVIG 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   


Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhheee......eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jlb B   1 MILVFLGPPGAGKGTQAKRLAKEKGFVHISTGDILREAVQKGTPLGKKAKEYMERGELVPDDLIIALIEEVFPKHGNVIFDGFPRTVKQAEALDEMLEKKGLKVDHVLLFEVPDEVVIERLSGRRINPETGEVYHVKYNPPPPGVKVIQREDDKPEVIKKRLEVYREQTAPLIEYYKKKGILRIIDASKPVEEVYRQVLEVIG 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4JLB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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  4jlb
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  2.7.4.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        KAD_AQUAE | O66490: 2rgx 2rh5 3sr0 4cf7 4ike 4jky 4jl5 4jl6 4jl8 4jla 4jld 4jlo 4jlp

(-) Related Entries Specified in the PDB File

4jl5 4jla 4jld 4jlo 4jlp