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(-) Description

Title :  CRYSTAL STRUCTURE OF ZEBRAFISH MTH1 IN COMPLEX WITH TH588
 
Authors :  M. Narwal, R. Gustafsson, L. Brautigam, L. Pudelko, A. -S. Jemth, H. Gad S. Karsten, J. Carreras-Puigvert, E. Homan, C. Berndt, U. W. Berglund T. Helleday, P. Stenmark
Date :  03 Feb 16  (Deposition) - 10 Feb 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Inhibitor, Complex, Mth1, Th588, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Brautigam, L. Pudelko, A. S. Jemth, H. Gad, M. Narwal, R. Gustafsson S. Karsten, J. Carreras Puigvert, E. Homan, C. Berndt, U. W. Berglund P. Stenmark, T. Helleday
Hypoxic Signaling And The Cellular Redox Tumor Environment Determine Sensitivity To Mth1 Inhibition.
Cancer Res. V. 76 2366 2016
PubMed-ID: 26862114  |  Reference-DOI: 10.1158/0008-5472.CAN-15-2380

(-) Compounds

Molecule 1 - NUDIX (NUCLEOSIDE DIPHOSPHATE LINKED MOIETY X)-TYPE MOTIF 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: NUDT1
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: UNCHARACTERIZED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
12GE2Ligand/IonN~4~-CYCLOPROPYL-6-(2,3-DICHLOROPHENYL)PYRIMIDINE-2,4-DIAMINE
2ACT1Ligand/IonACETATE ION
3GOL1Ligand/IonGLYCEROL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO45Ligand/IonSULFATE ION
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
12GE1Ligand/IonN~4~-CYCLOPROPYL-6-(2,3-DICHLOROPHENYL)PYRIMIDINE-2,4-DIAMINE
2ACT-1Ligand/IonACETATE ION
3GOL1Ligand/IonGLYCEROL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
12GE1Ligand/IonN~4~-CYCLOPROPYL-6-(2,3-DICHLOROPHENYL)PYRIMIDINE-2,4-DIAMINE
2ACT1Ligand/IonACETATE ION
3GOL-1Ligand/IonGLYCEROL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:8 , ASN A:33 , PHE A:72 , PHE A:74 , MET A:81 , TRP A:117 , ASP A:119 , ASP A:120 , SO4 A:202binding site for residue 2GE A 201
02AC2SOFTWARELEU A:9 , LYS A:23 , ASN A:33 , GLY A:34 , GLY A:36 , GLY A:37 , GLU A:56 , 2GE A:201 , HOH A:339 , LEU B:156binding site for residue SO4 A 202
03AC3SOFTWAREARG A:132 , HOH A:311 , HOH A:347 , ARG B:25binding site for residue SO4 A 203
04AC4SOFTWAREASP A:62 , THR A:63 , HIS A:65 , ASP A:89 , ASN A:90 , HOH A:308binding site for residue SO4 A 204
05AC5SOFTWAREASN A:90 , TYR A:91binding site for residue GOL A 205
06AC6SOFTWAREGLU A:46 , GLN A:47 , ARG A:50 , GLN A:115 , HOH A:310 , HOH A:324 , HOH A:340 , HOH A:356binding site for residue PEG A 206
07AC7SOFTWARETHR B:8 , PHE B:27 , ASN B:33 , PHE B:72 , MET B:81 , TRP B:117 , ASP B:119 , ASP B:120 , SO4 B:202binding site for residue 2GE B 201
08AC8SOFTWARELEU A:156 , LYS B:23 , GLY B:34 , GLY B:36 , GLY B:37 , GLU B:56 , 2GE B:201 , HOH B:324binding site for residue SO4 B 202
09AC9SOFTWAREARG A:25 , ARG B:132 , HOH B:334binding site for residue SO4 B 203
10AD1SOFTWAREHOH A:335 , LEU B:122 , HOH B:309 , HOH B:347binding site for residue ACT B 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HZX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HZX)

(-) 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:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..eeeeeee........ee.eeee.....hhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeeee............eeeeeee.hhhhhhhh..hhhhhhhhhhh...eeeeeeee...eeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hzx A   3 TSKLLTLVLVVQPGRVLLGMKKRGFGAGKWNGFGGKVQTGETIEQAARRELLEESGLTVDTLHKIGNIKFEFIGETELMDVHIFRADNYEGEPAESDEMRPQWFDIDKIPFSQMWADDILWFPLMLQKKRFLGYFKFQGHDVIVEHKLDEVEDL 156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152    


Chain B from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..eeeeeee........ee.eeee.....hhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeeee............eeeeeee.hhhhhhhh..hhhhhhhhhhh...eeeeeeee...eeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hzx B   3 TSKLLTLVLVVQPGRVLLGMKKRGFGAGKWNGFGGKVQTGETIEQAARRELLEESGLTVDTLHKIGNIKFEFIGETELMDVHIFRADNYEGEPAESDEMRPQWFDIDKIPFSQMWADDILWFPLMLQKKRFLGYFKFQGHDVIVEHKLDEVEDL 156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
   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 5HZX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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  5hzx
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 Related Entries

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(-) Related Entries Specified in the PDB File

4n1u 4N1U CONTAINS THE SAME INHIBITOR