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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 :  1.84
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, 13)

Asymmetric Unit (1, 13)
No.NameCountTypeFull Name
1GOL13Ligand/IonGLYCEROL
Biological Unit 1 (1, 52)
No.NameCountTypeFull Name
1GOL52Ligand/IonGLYCEROL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:114 , TYR A:115 , ARG A:144 , LYS A:362 , SER A:452 , ARG A:456 , TYR A:457 , HOH A:706 , HOH A:710binding site for residue GOL A 601
02AC2SOFTWAREASP A:252 , TYR A:253 , VAL A:288 , ASP A:289 , GLY A:310binding site for residue GOL A 602
03AC3SOFTWAREPHE A:283 , ASP A:284 , ILE A:286 , GLN A:322 , HIS A:323 , GLY A:324 , ILE A:325 , HOH A:721 , HOH A:742binding site for residue GOL A 603
04AC4SOFTWAREGLU A:374 , GLU A:378 , TYR A:434 , GLY A:438 , LEU A:440 , HOH A:734 , HOH A:791binding site for residue GOL A 604
05AC5SOFTWAREASP A:54 , HIS A:209 , LYS A:215 , SER A:251 , TYR A:255binding site for residue GOL A 605
06AC6SOFTWAREARG A:39 , TYR A:115 , ASN A:117 , LYS A:361 , ARG A:367 , ASP A:459 , GOL A:613 , HOH A:755binding site for residue GOL A 606
07AC7SOFTWAREASP A:257 , THR A:261 , PRO A:278 , TRP A:279 , GLN A:280 , HOH A:712 , HOH A:740binding site for residue GOL A 607
08AC8SOFTWAREVAL A:35 , VAL A:37 , TYR A:471 , TYR A:475 , ARG A:478 , GOL A:612 , HOH A:714binding site for residue GOL A 608
09AC9SOFTWAREASN A:117 , LEU A:118 , ARG A:134 , LYS A:344 , ARG A:446 , GOL A:613binding site for residue GOL A 609
10AD1SOFTWARETYR A:151 , GLN A:199 , ARG A:202binding site for residue GOL A 610
11AD2SOFTWAREPHE A:191 , HOH A:783binding site for residue GOL A 611
12AD3SOFTWAREARG A:34 , VAL A:35 , PHE A:36 , VAL A:37 , PRO A:485 , GOL A:608binding site for residue GOL A 612
13AD4SOFTWAREARG A:367 , GOL A:606 , GOL A:609 , HOH A:751 , HOH A:793binding site for residue GOL A 613

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L4Z)

(-) 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 5L4Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5L4Z)

(-) 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:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               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....eee......................eee.hhhhhhhhhh.hhh.eeeee.....hhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh........ee..eehhhhhhhhhhh.eee.hhhhhhhh....ee......hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l4z A   3 TSWSDRLQNAADMPANMDKHALKKYRREAYHRVFVNRSLAMEKIKCFGFDMDYTLAVYKSPEYESLGFELTVERLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERFYILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSWMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTICDLLGAKGKDILYIGDHIFGDILKSKKRQGWRTFLVIPELAQELHVWTDKSSLFEELQSLDIFLAESIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTLFASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHES 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       418       428       438       448       458       468       478       488
                                                                                                                                                                                                                                                                                                                                                                                                                                        401|                                                                      
                                                                                                                                                                                                                                                                                                                                                                                                                                         418
   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 5L4Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L4Z)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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    Lys A:292 - Pro A:293   [ 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 5l50

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L4Z)