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(-) Description

Title :  CRYSTAL STRUCTURE OF ENZYME IN PURINE METABOLISM
 
Authors :  A. Hnizda, P. Pachl, P. Rezacova
Date :  27 May 16  (Deposition) - 21 Sep 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Enzyme, Purine, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hnizda, J. Skerlova, M. Fabry, P. Pachl, M. Sinalova, L. Vrzal, P. Man, P. Novak, P. Rezacova, V. Veverka
Oligomeric Interface Modulation Causes Misregulation Of Purine 5 -Nucleotidase In Relapsed Leukemia.
Bmc Biol. V. 14 91 2016
PubMed-ID: 27756303  |  Reference-DOI: 10.1186/S12915-016-0313-Y

(-) Compounds

Molecule 1 - CYTOSOLIC PURINE 5'-NUCLEOTIDASE
    Chains: A
    EC Number: 3.1.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector Type: PLASMID
    Gene: NT5C2, NT5B, NT5CP, PNT5
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYTOSOLIC 5'-NUCLEOTIDASE II

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
Biological Unit 1 (1, 48)
No.NameCountTypeFull Name
1GOL48Ligand/IonGLYCEROL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:97 , GLU A:374 , GLU A:378 , TYR A:434 , HOH A:741 , HOH A:812 , HOH A:913binding site for residue GOL A 601
02AC2SOFTWAREPHE A:150 , TYR A:151 , ILE A:152 , ASN A:154 , HOH A:718 , HOH A:783binding site for residue GOL A 602
03AC3SOFTWAREASP A:52 , ASP A:54 , THR A:155 , PHE A:157 , ASP A:351 , HIS A:352 , HOH A:701 , HOH A:734 , HOH A:765binding site for residue GOL A 603
04AC4SOFTWAREALA A:114 , TYR A:115 , ARG A:144 , SER A:452 , ARG A:456 , TYR A:457 , HOH A:722binding site for residue GOL A 604
05AC5SOFTWAREPHE A:283 , ASP A:284 , LEU A:285 , ILE A:286 , GLY A:324 , ILE A:325 , HOH A:751binding site for residue GOL A 605
06AC6SOFTWAREASP A:252 , TYR A:253 , VAL A:288 , ASP A:289 , GLY A:310 , HOH A:704binding site for residue GOL A 606
07AC7SOFTWAREASP A:54 , TYR A:65 , HIS A:209 , LYS A:215 , SER A:251 , TYR A:255 , HOH A:702binding site for residue GOL A 607
08AC8SOFTWARELEU A:41 , ALA A:42 , LYS A:45 , ARG A:367 , HOH A:725 , HOH A:744binding site for residue GOL A 608
09AC9SOFTWAREPHE A:157 , ARG A:202 , ASP A:206 , HIS A:209 , TYR A:210 , HOH A:740binding site for residue GOL A 609
10AD1SOFTWARETHR A:104 , THR A:147 , GLU A:148 , PHE A:150 , TYR A:151 , ARG A:195 , GLN A:199binding site for residue GOL A 610
11AD2SOFTWAREASP A:257 , THR A:261 , PRO A:278 , GLN A:280 , HOH A:761binding site for residue GOL A 611
12AD3SOFTWARELEU A:468 , TYR A:471 , PRO A:472 , PHE A:473binding site for residue GOL A 612

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L50)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:62 -Pro A:63
2Lys A:292 -Pro A:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L50)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L50)

(-) Exons   (0, 0)

(no "Exon" information available for 5L50)

(-) 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:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhhhhhhhhhhh.ee...ee.hhh.eeee...........hhhhhhhhhhhhhhhhhh..hhhhhhh..........eeee....eeeee.....eeeeee..ee.hhhhhhhhh............eeee.hhhhhhhhhhhhhhhhhhhhh...eee..eeee..eeeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhheeeee...hhhhhhhhhhhhh.............hhhhhh.eeee....hhhhh....eeeee....ee..............eee.hhhhhhhhhh.hhh.eeeee....hhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhh.eee.hhhhhhhh....ee......hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l50 A   3 TSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFDMDYTLAVYKSPEYESLGFELTVERLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERFYILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPEFAQELHVWTDKSSLFEELQSLDIFLAELSSIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTLFASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES 488
                                    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       352       362       372       382       392       402|      426       436       446       456       466       476       486  
                                                                                                                                                                                                                                                                                                                                                                                                                                         402|                                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                          417
   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 5L50)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L50)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L50)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys A:292 - Pro A:293   [ RasMol ]  
    Ser A:62 - Pro A:63   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        5NTC_HUMAN | P49902: 2j2c 2jc9 2jcm 2xcv 2xcw 2xcx 2xjb 2xjc 2xjd 2xje 2xjf 4h4b 5cqz 5cr7 5k7y 5l4z

(-) Related Entries Specified in the PDB File

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