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(-) Description

Title :  HUMAN ADENOSINE KINASE IN COMPLEX WITH INHIBITOR
 
Authors :  J. Brynda, J. Dostal, I. Pichova, M. Hodcek
Date :  16 Dec 13  (Deposition) - 26 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Adenosine Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Snasel, P. Naus, J. Dostal, A. Hnizda, J. Fanfrlik, J. Brynda, A. Bourderioux, M. Dusek, H. Dvorakova, J. Stolarikova, H. Zabranska R. Pohl, P. Konecny, P. Dzubak, I. Votruba, M. Hajduch, P. Rezacova, V. Veverka, M. Hocek, I. Pichova
Structural Basis For Inhibition Of Mycobacterial And Human Adenosine Kinase By 7-Substituted 7-(Het)Aryl-7-Deazaadenin Ribonucleosides
J. Med. Chem. V. 57 8268 2014
PubMed-ID: 25259627  |  Reference-DOI: 10.1021/JM500497V

(-) Compounds

Molecule 1 - ADENOSINE KINASE
    Chains: A, B
    EC Number: 2.7.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 17-362
    Gene: ADK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AK, ADENOSINE 5'-PHOSPHOTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1HO43Ligand/Ion5-ETHYNYL-7-(BETA-D-RIBOFURANOSYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1HO43Ligand/Ion5-ETHYNYL-7-(BETA-D-RIBOFURANOSYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1HO42Ligand/Ion5-ETHYNYL-7-(BETA-D-RIBOFURANOSYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HO41Ligand/Ion5-ETHYNYL-7-(BETA-D-RIBOFURANOSYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , ASN A:14 , THR A:66 , HO4 A:403BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREHOH A:506 , HOH A:507 , HOH A:508 , HOH A:509 , HOH A:510BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREASN A:14 , LEU A:16 , ASP A:18 , ILE A:39 , LEU A:40 , GLY A:63 , GLY A:64 , SER A:65 , ASN A:68 , PHE A:170 , ASN A:296 , GLY A:297 , ASP A:300 , MG A:401 , HOH A:501BINDING SITE FOR RESIDUE HO4 A 403
4AC4SOFTWARETHR A:265 , GLY A:267 , ARG A:268 , VAL A:284 , ASP A:286 , GLN A:287 , ALA A:298 , GLY A:299 , HIS A:324 , ALA A:327 , ILE A:331 , HOH A:505BINDING SITE FOR RESIDUE HO4 A 404
5AC5SOFTWAREASN B:14 , THR B:66 , ALA B:168 , HO4 B:403BINDING SITE FOR RESIDUE MG B 401
6AC6SOFTWAREHOH B:504 , HOH B:505 , HOH B:506 , HOH B:507BINDING SITE FOR RESIDUE MG B 402
7AC7SOFTWAREASN B:14 , LEU B:16 , ASP B:18 , ILE B:39 , GLY B:63 , GLY B:64 , SER B:65 , ASN B:68 , ALA B:136 , PHE B:170 , ASN B:296 , GLY B:297 , ASP B:300 , MG B:401 , HOH B:508BINDING SITE FOR RESIDUE HO4 B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O1L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:79 -Pro A:80
2Gln B:79 -Pro B:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O1L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O1L)

(-) Exons   (0, 0)

(no "Exon" information available for 4O1L)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...eeeeeee.hhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..eeeeeeehhhhhhhhhhhh..hhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhh.....hhhhhhhhhhh..........eeeeee..eeeeee....eeee.........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o1l A   4 LRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLDQDQKIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASIII 331
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283      |295       305       315       325      
                                                                                                                                                                                                                                                                                                                        290|                                      
                                                                                                                                                                                                                                                                                                                         293                                      


Chain B from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee...eeeeeee.hhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..eeeeeeehhhhhhhhhhhh..hhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhh.....hhhhhhhhhhh..........eeeeee..eeeeee....eeee....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o1l B   0 APQALRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASIIIRRTGCTFPEKPDFH 345
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     ||296       306       316       326       336         
                                                                                                                                                                                                                                                                                                                       285|                                                    
                                                                                                                                                                                                                                                                                                                        293
   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 4O1L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O1L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O1L)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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        ADK_HUMAN | P55263: 1bx4 2i6a 2i6b

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4pvv