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(-) Description

Title :  STRUCTURE OF TRYPANOSOMA BRUCEI BRUCEI ADENOSINE KINASE IN COMPLEX WITH ADENOSINE AND AMPPNP
 
Authors :  J. Timm, D. Gonzalez-Pacanowska, K. S. Wilson
Date :  01 Oct 13  (Deposition) - 15 Jan 14  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
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 :  Anion Hole, Adenosine Kinase, Adenosine, Amppnp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Timm, D. Gonzalez-Pacanowska, K. S. Wilson
Structures Of Adenosine Kinase From Trypanosoma Brucei Brucei.
Acta Crystallogr F Struct V. 70 34 2014 Biol Commun
PubMed-ID: 24419613  |  Reference-DOI: 10.1107/S2053230X13033621

(-) Compounds

Molecule 1 - ADENOSINE KINASE
    Chains: A, B, C, D
    EC Number: 2.7.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TB927.6.2360
    Organism Scientific: TRYPANOSOMA BRUCEI BRUCEI
    Organism Taxid: 999953
    Strain: 927/4 GUTAT10.1

 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ADN4Ligand/IonADENOSINE
2ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
3EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:13 , LEU A:15 , ASP A:17 , LEU A:39 , GLY A:63 , SER A:64 , ASN A:67 , ALA A:136 , PHE A:169 , ASP A:299BINDING SITE FOR RESIDUE ADN A 401
02AC2SOFTWAREASN A:222 , THR A:264 , ARG A:265 , ASP A:266 , THR A:270 , GLN A:288 , MET A:294 , ALA A:297 , GLY A:298 , HIS A:323 , ALA A:326 , GLN A:327 , ILE A:330 , EDO A:403 , HOH A:510BINDING SITE FOR RESIDUE ADP A 402
03AC3SOFTWAREASN A:195 , ALA A:221 , ASN A:222 , GLU A:225 , THR A:264 , GLY A:298 , ADP A:402BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWAREASN B:13 , LEU B:15 , ASP B:17 , LEU B:39 , GLY B:63 , SER B:64 , ASN B:67 , ALA B:136 , PHE B:169 , ASP B:299 , HOH B:511BINDING SITE FOR RESIDUE ADN B 401
05AC5SOFTWAREASN B:222 , THR B:264 , ARG B:265 , ASP B:266 , THR B:270 , VAL B:283 , GLN B:288 , MET B:294 , ALA B:297 , GLY B:298 , HIS B:323 , ALA B:326 , GLN B:327 , ILE B:330 , EDO B:403 , HOH B:504 , HOH B:512BINDING SITE FOR RESIDUE ADP B 402
06AC6SOFTWAREASN B:195 , GLU B:225 , THR B:264 , GLY B:298 , ADP B:402 , HOH B:535BINDING SITE FOR RESIDUE EDO B 403
07AC7SOFTWAREASN C:13 , LEU C:15 , ASP C:17 , LEU C:39 , GLY C:63 , SER C:64 , ASN C:67 , ALA C:136 , PHE C:169 , GLY C:296 , ASP C:299BINDING SITE FOR RESIDUE ADN C 401
08AC8SOFTWAREASN C:222 , THR C:264 , ARG C:265 , ASP C:266 , ILE C:267 , THR C:270 , VAL C:283 , GLN C:288 , MET C:294 , GLY C:298 , HIS C:323 , ALA C:326 , GLN C:327 , ILE C:330 , HOH C:512BINDING SITE FOR RESIDUE ADP C 402
09AC9SOFTWAREASN D:13 , LEU D:15 , ASP D:17 , LEU D:39 , GLY D:63 , SER D:64 , ASN D:67 , LEU D:134 , ALA D:136 , PHE D:169 , ASN D:295 , GLY D:296 , ASP D:299BINDING SITE FOR RESIDUE ADN D 401
10BC1SOFTWAREASN D:222 , THR D:264 , ARG D:265 , ASP D:266 , THR D:270 , VAL D:283 , GLN D:288 , MET D:294 , ALA D:297 , GLY D:298 , HIS D:323 , ALA D:326 , GLN D:327 , ILE D:330 , HOH D:514BINDING SITE FOR RESIDUE ADP D 402

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:239 -D:239
2B:239 -C:239

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N09)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N09)

(-) Exons   (0, 0)

(no "Exon" information available for 4N09)

(-) 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:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4n09a_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee...eeeeeee.hhhhhhhh......eee.hhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh...eeee.eee.hhhhhhhhhhhhhhh.ee..eee.....eeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh....hhhhhhhhhhhh.........eeeeee..eeeeeee..eeeee.....hhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n09 A   1 MSSAPLRVYVQCNPLLDVSAHVSDEFLVKYGLERGTAILLSERQKGIFDDIEKMPNVRYVPGGSGLNVARVAQWMQQAYKGKFVTYVGCIADDRYGKVLKEAAEHEGIVMAVEHTTKAGSGACAVCITGKERTLVADLGAANHLSSEHMRSPAVVRAMDESRIFYFSGFTLTVDVNHVLQACRKAREVDGLFMINLSAPFIMQFFSAQLGEVLPYTDIIVANRHEAKEFANMMKWDTDCVEEIARRAVSEVPYTGTKGRVVVFTRDIESTVLATKDGVETVPVPQLDQDKVIDMNGAGDAFMGGFLSAYAVGKDLRRCCETGHYTAQEVIQRDGCSFPEKPSFSP 345
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340     


Chain B from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4n09b_ B: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee...eeeeeee.hhhhhhhh......eee.hhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh...eeee.ee..hhhhhhhhhhhhhhh.ee..ee......eeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhh.....hhhhhhhhhhhh.........eeeeee..eeeeeee..eeeee.....hhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n09 B   1 MSSAPLRVYVQCNPLLDVSAHVSDEFLVKYGLERGTAILLSERQKGIFDDIEKMPNVRYVPGGSGLNVARVAQWMQQAYKGKFVTYVGCIADDRYGKVLKEAAEHEGIVMAVEHTTKAGSGACAVCITGKERTLVADLGAANHLSSEHMRSPAVVRAMDESRIFYFSGFTLTVDVNHVLQACRKAREVDGLFMINLSAPFIMQFFSAQLGEVLPYTDIIVANRHEAKEFANMMKWDTDCVEEIARRAVSEVPYTGTKGRVVVFTRDIESTVLATKDGVETVPVPQLDQDKVIDMNGAGDAFMGGFLSAYAVGKDLRRCCETGHYTAQEVIQRDGCSFPEKPSFSP 345
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340     


Chain C from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4n09c_ C: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee...eeeeeee.hhhhhhhh......eee.hhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh...eeee.eee.hhhhhhhhhhhhhhh.ee..eee.....eeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhh.....hhhhhhhhhhhh.........eeeeee..eeeeeee..eeeee.....hhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n09 C   1 MSSAPLRVYVQCNPLLDVSAHVSDEFLVKYGLERGTAILLSERQKGIFDDIEKMPNVRYVPGGSGLNVARVAQWMQQAYKGKFVTYVGCIADDRYGKVLKEAAEHEGIVMAVEHTTKAGSGACAVCITGKERTLVADLGAANHLSSEHMRSPAVVRAMDESRIFYFSGFTLTVDVNHVLQACRKAREVDGLFMINLSAPFIMQFFSAQLGEVLPYTDIIVANRHEAKEFANMMKWDTDCVEEIARRAVSEVPYTGTKGRVVVFTRDIESTVLATKDGVETVPVPQLDQDKVIDMNGAGDAFMGGFLSAYAVGKDLRRCCETGHYTAQEVIQRDGCSFPEKPSFSP 345
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340     


Chain D from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4n09d_ D: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee...eeeeeee.hhhhhhhh......eee.hhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh...eeee.eee.hhhhhhhhhhhhhh..ee..eee.....eeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhh.....hhhhhhhhhhhh.........eeeeee..eeeeeee..eeeee.....hhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4n09 D   3 SAPLRVYVQCNPLLDVSAHVSDEFLVKYGLERGTAILLSERQKGIFDDIEKMPNVRYVPGGSGLNVARVAQWMQQAYKGKFVTYVGCIADDRYGKVLKEAAEHEGIVMAVEHTTKAGSGACAVCITGKERTLVADLGAANHLSSEHMRSPAVVRAMDESRIFYFSGFTLTVDVNHVLQACRKAREVDGLFMINLSAPFIMQFFSAQLGEVLPYTDIIVANRHEAKEFANMMKWDTDCVEEIARRAVSEVPYTGTKGRVVVFTRDIESTVLATKDGVETVPVPQLDQDKVIDMNGAGDAFMGGFLSAYAVGKDLRRCCETGHYTAQEVIQRDGCSFPEKPSFS 344
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342
   Legend:   → Mismatch (orange background)
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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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N09)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N09)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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        Q584S0_TRYB2 | Q584S0: 2xtb 3otx 4n08

(-) Related Entries Specified in the PDB File

4n08 APO ADENOSINE KINASE FROM TRYPANOSOMA BRUCEI BRUCEI