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(-) Description

Title :  LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH HEPTAMOLYBDATE AND OCTAMOLYBDATE
 
Authors :  M. Zebisch, P. Schaefer, N. Straeter
Date :  27 Jun 13  (Deposition) - 12 Feb 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Apyrase, Purinergic Signalling, Keggin, Transition State, Adpase, Cd39 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zebisch, M. Krauss, P. Schafer, N. Strater
Structures Of Legionella Pneumophila Ntpdase1 In Complex With Polyoxometallates.
Acta Crystallogr. , Sect. D V. 70 1147 2014
PubMed-ID: 24699658  |  Reference-DOI: 10.1107/S1399004714001916

(-) Compounds

Molecule 1 - ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LEGIONELLA PNEUMOPHILA
    Organism Taxid: 446
    Synonym: NTPDASE1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 33)

Asymmetric/Biological Unit (11, 33)
No.NameCountTypeFull Name
16LL2Ligand/IonTETRAKIS-(MU-OXO)-DECA-OXO-TRIMOLYBDENUM
28M02Ligand/IonBIS(MU4-OXO)-TETRAKIS(MU3-OXO)-HEXAKIS(MU2-OXO)-HEXADECAOXO-OCTAMOLYBDENUM (VI)
3CL2Ligand/IonCHLORIDE ION
4EDO4Ligand/Ion1,2-ETHANEDIOL
5GOL7Ligand/IonGLYCEROL
6M274Ligand/IonCYCLODIMOLYBDOXAN-2,2,2,2,4,4,4,4-OCTOL
7MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
8MG5Ligand/IonMAGNESIUM ION
9MO72Ligand/IonBIS(MU4-OXO)-BIS(MU3-OXO)-OCTAKIS(MU2-OXO)-DODECAOXO-HEPTAMOLYBDENUM (VI)
10MOO2Ligand/IonMOLYBDATE ION
11NA1Ligand/IonSODIUM ION

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:233 , HIS A:236 , HOH A:2131 , GLU B:233 , HIS B:236BINDING SITE FOR RESIDUE NA A1402
02AC2SOFTWAREGLY A:51 , SER A:52 , THR A:118 , ALA A:119 , GLY A:120 , GLU A:159 , GLY A:189 , ALA A:190 , SER A:191 , MG A:1404 , HOH A:2003 , HOH A:2062 , HOH A:2092 , HOH A:2093 , HOH A:2227BINDING SITE FOR RESIDUE MOO A1403
03AC3SOFTWAREMOO A:1403 , HOH A:2003 , HOH A:2004 , HOH A:2093 , HOH A:2101 , HOH A:2227BINDING SITE FOR RESIDUE MG A1404
04AC4SOFTWAREHIS A:224 , PHE A:226 , VAL A:275 , HIS A:276 , LYS A:277 , GLN A:281 , HOH A:2126 , GLU B:267BINDING SITE FOR RESIDUE MES A1405
05AC5SOFTWAREARG A:122 , GLY A:156 , HOH A:2067 , ASN B:240 , ASP B:253BINDING SITE FOR RESIDUE CL B1402
06AC6SOFTWAREGLN A:307 , HOH A:2185 , HOH A:2186 , HOH A:2187 , HOH A:2229BINDING SITE FOR RESIDUE MG A1406
07AC7SOFTWAREGLN A:231 , THR A:232 , GLN A:349 , HOH A:2128 , HOH A:2137 , HOH A:2230 , PRO B:125BINDING SITE FOR RESIDUE GOL A1407
08AC8SOFTWARESER A:306 , GLN A:307 , TYR A:341 , ASP A:343 , ASP A:344 , EDO A:1409 , HOH A:2231BINDING SITE FOR RESIDUE M27 A1408
09AC9SOFTWAREASP A:343 , ASP A:344 , M27 A:1408BINDING SITE FOR RESIDUE EDO A1409
10BC1SOFTWAREALA A:104 , HIS A:109 , TRP A:139 , GLN A:143 , SER A:144 , GLN A:145 , TRP A:146 , EDO A:1411BINDING SITE FOR RESIDUE M27 A1410
11BC2SOFTWAREGLN A:143 , SER A:144 , M27 A:1410BINDING SITE FOR RESIDUE EDO A1411
12BC3SOFTWAREASN A:157 , ASP A:158 , LEU A:161 , HIS A:207 , VAL A:210 , 6LL A:1412 , HOH A:2232BINDING SITE FOR RESIDUE GOL A1413
13BC4SOFTWARETYR A:116 , LYS A:152 , ILE A:154 , ASP A:158 , 6LL A:1412BINDING SITE FOR RESIDUE EDO A1414
14BC5SOFTWAREARG A:56 , LYS A:80 , LYS A:82 , GLU A:345 , ASN A:381 , HOH A:2206 , HOH A:2207 , 8M0 B:1403BINDING SITE FOR RESIDUE MO7 A1415
15BC6SOFTWARELYS A:82 , GLU A:345 , TYR A:346 , MO7 A:1415 , HOH A:2045 , HOH A:2206 , HOH A:2208 , PRO B:125 , SER B:127 , GLN B:128 , LYS B:131 , HOH B:2060 , HOH B:2063 , HOH B:2204BINDING SITE FOR RESIDUE 8M0 B1403
16BC7SOFTWAREHOH A:2132 , HOH A:2134 , HOH B:2115 , HOH B:2116BINDING SITE FOR RESIDUE MG A1418
17BC8SOFTWAREGLY B:51 , SER B:52 , THR B:118 , ALA B:119 , GLY B:120 , GLU B:159 , GLY B:189 , ALA B:190 , SER B:191 , MG B:1405 , HOH B:2003 , HOH B:2050 , HOH B:2080 , HOH B:2081 , HOH B:2087 , HOH B:2205BINDING SITE FOR RESIDUE MOO B1404
18BC9SOFTWAREMOO B:1404 , HOH B:2003 , HOH B:2005 , HOH B:2080 , HOH B:2087 , HOH B:2205BINDING SITE FOR RESIDUE MG B1405
19CC1SOFTWARESER A:241 , GLU A:267 , HOH A:2142 , HIS B:224 , PHE B:226 , VAL B:275 , HIS B:276 , GLN B:281BINDING SITE FOR RESIDUE MES B1406
20CC2SOFTWAREASN A:240 , ASP A:253 , ARG B:122 , GLY B:156BINDING SITE FOR RESIDUE CL A1416
21CC3SOFTWAREGLN B:307 , HOH B:2154 , HOH B:2155 , HOH B:2156 , HOH B:2206BINDING SITE FOR RESIDUE MG B1407
22CC4SOFTWAREPRO A:125 , HOH A:2068 , HOH A:2069 , GLN B:231 , THR B:232 , GLN B:349 , HOH B:2112 , HOH B:2207BINDING SITE FOR RESIDUE GOL B1408
23CC5SOFTWAREGLN B:307 , TYR B:341 , ASP B:343 , ASP B:344 , GOL B:1410 , HOH B:2180BINDING SITE FOR RESIDUE M27 B1409
24CC6SOFTWARESER B:305 , ASP B:343 , ASP B:344 , M27 B:1409BINDING SITE FOR RESIDUE GOL B1410
25CC7SOFTWAREALA B:104 , HIS B:109 , TRP B:139 , GLN B:143 , SER B:144 , GLN B:145 , TRP B:146 , GOL B:1412 , HOH B:2048BINDING SITE FOR RESIDUE M27 B1411
26CC8SOFTWAREGLN A:319 , PRO A:369 , HOH A:2216 , GLN B:142 , GLN B:143 , SER B:144 , M27 B:1411BINDING SITE FOR RESIDUE GOL B1412
27CC9SOFTWAREHOH A:2159 , LYS B:152 , ILE B:154 , THR B:155 , ASP B:158 , HIS B:391 , GOL B:1414 , EDO B:1415 , HOH B:2197BINDING SITE FOR RESIDUE 6LL B1413
28DC1SOFTWAREHOH A:2159 , ASN B:157 , ASP B:158 , LEU B:161 , HIS B:207 , VAL B:210 , 6LL B:1413BINDING SITE FOR RESIDUE GOL B1414
29DC2SOFTWARETYR B:116 , LYS B:152 , ILE B:154 , ASP B:158 , 6LL B:1413BINDING SITE FOR RESIDUE EDO B1415
30DC3SOFTWARE8M0 A:1417 , HOH A:2236 , HOH A:2237 , ARG B:56 , LYS B:80 , LYS B:82 , GLU B:345 , ASN B:381 , HOH B:2019 , HOH B:2184 , HOH B:2208 , HOH B:2209 , HOH B:2210BINDING SITE FOR RESIDUE MO7 B1416
31DC4SOFTWAREPRO A:125 , SER A:127 , GLN A:128 , LYS A:131 , HOH A:2071 , HOH A:2075 , HOH A:2234 , HOH A:2235 , HOH A:2237 , HOH A:2238 , HOH A:2239 , HOH A:2240 , LYS B:82 , GLU B:345 , TYR B:346 , MO7 B:1416BINDING SITE FOR RESIDUE 8M0 A1417
32DC5SOFTWAREASP B:49 , GLY B:51 , THR B:53 , GLY B:54 , ARG B:56 , LYS B:80 , HOH B:2004 , HOH B:2009 , HOH B:2205BINDING SITE FOR RESIDUE GOL B1417
33DC6SOFTWARELYS A:152 , ILE A:154 , THR A:155 , ASP A:158 , PHE A:162 , HIS A:391 , GOL A:1413 , EDO A:1414 , HOH A:2086 , HOH A:2090 , HOH A:2221 , HOH A:2232BINDING SITE FOR RESIDUE 6LL A1412

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:39 -A:44
2A:244 -A:264
3A:330 -A:351
4B:39 -B:44
5B:244 -B:264
6B:330 -B:351

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:82 -Pro A:83
2Lys B:82 -Pro B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BVP)

(-) Sequences/Alignments

Asymmetric/Biological 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:365
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:365
                                                                                                                                                                                                                                                                                                                                                                                              393        
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386      |  -     
         Q5ZUA2_LEGPH    37 NPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA--------   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeeee..eeeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh.......eeeeeehhhhhh.hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhh.........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeehhhhhhh.........eeehhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh.........eeee.hhhhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bvp A  37 NPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRALEHHHHHH 401
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396     


Chain B from PDB  Type:PROTEIN  Length:365
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:365
                                                                                                                                                                                                                                                                                                                                                                                              393        
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386      |  -     
         Q5ZUA2_LEGPH    37 NPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA--------   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeeee..eeeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh.......eeeeeehhhhhh.hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhh.........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhh...hhhhhhhhhhhhh...eeeeeehhhhhhh.........eeehhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh.........eeee.hhhhh..hhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bvp B  37 NPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRALEHHHHHH 401
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396
   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 4BVP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  4bvp
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  Q5ZUA2_LEGPH | Q5ZUA2
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 Related Entries

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

UniProtKB/TrEMBL
        Q5ZUA2_LEGPH | Q5ZUA2: 3aap 3aaq 3aar 4br4 4br7 4br9 4bra 4brc 4brd 4bre 4brf 4brg 4brh 4bri 4brk 4brl 4brm 4brn 4bro 4brp 4brq 4bvo

(-) Related Entries Specified in the PDB File

4bvo LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM VI (PART- OPEN) IN COMPLEX WITH POLYTUNGSTATE POM-1