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(-) Description

Title :  LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, AMPNP COMPLEX
 
Authors :  M. Zebisch, P. Schaefer, P. Lauble, N. Straeter
Date :  04 Jun 13  (Deposition) - 17 Jul 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Apyrase, Atpase, Adpase, Cd39, Purinergic Signalling, Domain Rotation, Transition State, Ntpdase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zebisch, M. Krauss, P. Schaefer, P. Lauble, N. Straeter
Crystallographic Snapshots Along The Reaction Pathway Of Nucleoside Triphosphate Diphosphohydrolases
Structure V. 21 1460 2013
PubMed-ID: 23830739  |  Reference-DOI: 10.1016/J.STR.2013.05.016

(-) Compounds

Molecule 1 - ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
    Chains: A
    EC Number: 3.6.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 37-393
    Organism Scientific: LEGIONELLA PNEUMOPHILA
    Organism Taxid: 446
    Synonym: NTPDASE1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1AU11Ligand/Ion5'-O-[(R)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]ADENOSINE
2CL2Ligand/IonCHLORIDE ION
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1AU12Ligand/Ion5'-O-[(R)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]ADENOSINE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:53 , GLN A:231 , GLY A:299 , ASN A:302 , LEU A:303 , TYR A:346 , TYR A:350 , LEU A:353 , TYR A:357 , HOH A:2153 , HOH A:2285 , HOH A:2309BINDING SITE FOR RESIDUE AU1 A1394
2AC2SOFTWAREARG A:122 , GLY A:156 , ASP A:253 , HOH A:2130BINDING SITE FOR RESIDUE CL A1395
3AC3SOFTWAREHOH A:2185 , HOH A:2186 , HOH A:2311 , HOH A:2312BINDING SITE FOR RESIDUE MG A 405
4AC4SOFTWAREASN A:327 , GLN A:328 , HOH A:2272BINDING SITE FOR RESIDUE CL A1396

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:39 -A:44
2A:244 -A:264
3A:330 -A:351

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:82 -Pro A:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BR7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BR7)

(-) Exons   (0, 0)

(no "Exon" information available for 4BR7)

(-) 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:356
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:356
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387      
         Q5ZUA2_LEGPH    38 PCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA 393
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee....eeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh......eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhh..........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeehhhhhhh.........eeehhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh.........eeee.hhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4br7 A  38 PCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA 393
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387
   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  (0, 0)

(no "SCOP Domain" information available for 4BR7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BR7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BR7)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5ZUA2_LEGPH | Q5ZUA2)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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  4br7
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  Q5ZUA2_LEGPH | Q5ZUA2
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  3.6.1.5
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 Related Entries

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

UniProtKB/TrEMBL
        Q5ZUA2_LEGPH | Q5ZUA2: 3aap 3aaq 3aar 4br4 4br9 4bra 4brc 4brd 4bre 4brf 4brg 4brh 4bri 4brk 4brl 4brm 4brn 4bro 4brp 4brq 4bvo 4bvp

(-) Related Entries Specified in the PDB File

4bqz RAT NTPDASE2 IN COMPLEX WITH MG GMPPNP
4br0 RAT NTPDASE2 IN COMPLEX WITH CA AMPNP
4br2 RAT NTPDASE2 IN COMPLEX WITH CA UMPPNP
4br4 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO
4br5 RNNTPDASE2 IN COMPLEX WITH ZNAMPPNP
4br9 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, APO
4bra LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPPNP COMPLEX
4brc LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPNP COMPLEX
4brd LEGIONELLA PNEUMOPHILA NTPDASE1 Q193E CRYSTAL FORM II, CLOSED, MG AMPPNP COMPLEX
4bre LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH TRANSITION STATE MIMIC ADENOSINE 5' PHOSPHOVANADATE
4brf LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH A DISTORTED ORTHOMOLYBDATE ION AND AMP
4brg LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG GMPPNP
4brh LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG AND THIAMINE PHOSPHOVANADATE
4bri LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG UMPPNP
4brk LEGIONELLA PNEUMOPHILA NTPDASE1 N302Y VARIANT CRYSTAL FORM III (CLOSED) IN COMPLEX WITH MG UMPPNP
4brl LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN COMPLEX WITH TRANSITION STATE MIMI GUANOSINE 5'- PHOSPHOVANADATE
4brm SULFUR SAD PHASING OF THE LEGIONELLA PNEUMOPHILA NTPDASE1 - CRYSTAL FORM III (CLOSED) IN COMPLEX WITH SULFATE
4brn LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN COMPLEX WITH MG AMP
4bro LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM IV (PART- OPEN)
4brp LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM V (PART- OPEN)
4brq LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, IN COMPLEX WITH TWO PHOSPHATES BOUND TO ACTIVE SITE MG AND PRODUCT AMP