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(-) Description

Title :  STRUCTURE OF HUMAN MTH1 IN COMPLEX WITH TH588
 
Authors :  R. P-A. Berntsson, A. Jemth, R. Gustafsson, L. M. Svensson, T. Helleday P. Stenmark
Date :  04 Oct 13  (Deposition) - 16 Apr 14  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidised Nucleotide Degradation, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Gad, T. Koolmeister, A. S. Jemth, S. Eshtad, S. A. Jacques, C. E. Strom, L. M. Svensson, N. Schultz, T. Lundback, B. O. Einarsdottir, A. Saleh, C. Gokturk, P. Baranczewski, R. Svensson, R. P. Berntsson, R. Gustafsson, K. Stromberg, K. Sanjiv, M. C. Jacques-Cordonnier, M. Desroses, A. L. Gustavsson, R. Olofsson F. Johansson, E. J. Homan, O. Loseva, L. Brautigam, L. Johansson, A. Hoglund, A. Hagenkort, T. Pham, M. Altun, F. Z. Gaugaz, S. Vikingsson, B. Evers, M. Henriksson, K. S. Vallin, O. A. Wallner, L. G. Hammarstrom, E. Wiita, I. Almlof, C. Kalderen, H. Axelsson, T. Djureinovic, J. C. Puigvert, M. Haggblad, F. Jeppsson, U. Martens, C. Lundin, B. Lundgren, I. Granelli, A. J. Jensen, P. Artursson, J. A. Nilsson, P. Stenmark, M. Scobie, U. W. Berglund, T. Helleday
Mth1 Inhibition Eradicates Cancer By Preventing Sanitation Of The Dntp Pool.
Nature V. 508 215 2014
PubMed-ID: 24695224  |  Reference-DOI: 10.1038/NATURE13181

(-) Compounds

Molecule 1 - 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.55, 3.6.1.56
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 42-197
    Gene: NUDT1, MTH1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 2-HYDROXY-DATP DIPHOSPHATASE, 8-OXO-DGTPASE, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 1, NUDIX MOTIF 1

 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  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
12GE2Ligand/IonN~4~-CYCLOPROPYL-6-(2,3-DICHLOROPHENYL)PYRIMIDINE-2,4-DIAMINE
2SO412Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
12GE1Ligand/IonN~4~-CYCLOPROPYL-6-(2,3-DICHLOROPHENYL)PYRIMIDINE-2,4-DIAMINE
2SO47Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
12GE1Ligand/IonN~4~-CYCLOPROPYL-6-(2,3-DICHLOROPHENYL)PYRIMIDINE-2,4-DIAMINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:8 , PHE A:27 , ASN A:33 , PHE A:72 , TRP A:117 , ASP A:119 , ASP A:120 , TRP A:123 , PHE A:139BINDING SITE FOR RESIDUE 2GE A 201
02AC2SOFTWARELEU A:9 , LYS A:23 , GLY A:34 , GLY A:36 , GLU A:56 , MET A:101 , HOH A:304BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREGLU A:77 , HIS B:65 , LYS B:66 , LYS B:132 , SO4 B:204BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWARETYR A:122 , TYR A:148 , HOH A:335 , LYS B:24 , TYR B:136 , LYS B:138 , SO4 B:203BINDING SITE FOR RESIDUE SO4 A 204
05AC5SOFTWAREALA A:63 , HIS A:65 , THR A:88 , ASP A:89 , SER A:90 , HOH A:354 , GLN B:142BINDING SITE FOR RESIDUE SO4 A 205
06AC6SOFTWARELYS A:23 , GLY A:26 , PHE A:27 , LYS B:114BINDING SITE FOR RESIDUE SO4 A 206
07AC7SOFTWARELYS A:66 , HIS A:134 , ARG B:17 , HOH B:330BINDING SITE FOR RESIDUE SO4 A 207
08AC8SOFTWAREPHE A:113 , SER A:121 , PRO A:125BINDING SITE FOR RESIDUE SO4 A 208
09AC9SOFTWARETYR B:7 , THR B:8 , PHE B:27 , ASN B:33 , PHE B:72 , PHE B:74 , MET B:81 , TRP B:117 , ASP B:119 , ASP B:120 , TRP B:123 , PHE B:139 , SO4 B:202 , HOH B:369BINDING SITE FOR RESIDUE 2GE B 201
10BC1SOFTWARELYS B:23 , ASN B:33 , GLY B:34 , GLY B:36 , GLU B:56 , GLU B:100 , MET B:101 , 2GE B:201 , HOH B:307BINDING SITE FOR RESIDUE SO4 B 202
11BC2SOFTWARETYR A:122 , ILE A:145 , SO4 A:204 , LYS B:24 , GLU B:97 , SER B:98 , ASP B:99BINDING SITE FOR RESIDUE SO4 B 203
12BC3SOFTWAREPHE A:27 , PHE A:74 , GLU A:77 , GLY A:141 , GLN A:142 , SO4 A:203 , HIS B:65BINDING SITE FOR RESIDUE SO4 B 204
13BC4SOFTWARESER A:121 , TYR A:122 , ARG B:25 , ASP B:99BINDING SITE FOR RESIDUE SO4 B 205
14BC5SOFTWAREGLN A:142 , ALA B:63 , HIS B:65 , THR B:88 , ASP B:89 , SER B:90 , HOH B:352 , HOH B:401BINDING SITE FOR RESIDUE SO4 B 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N1U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N1U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N1U)

(-) Exons   (0, 0)

(no "Exon" information available for 4N1U)

(-) 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:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee...eeeeeee........ee.eeee.....hhhhhhhhhhhhhhh.ee...eeeeeeeeee.....eeeeeeeee..ee........eeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n1u A   3 ASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDT 155
                                    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 ..eeeeeeeeee...eeeeeee........ee..........hhhhhhhhhhhhhhh......eeeeeeeeee.....eeeeeeeee............eeeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n1u B   2 GASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDT 155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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 4N1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N1U)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        8ODP_HUMAN | P36639: 1iry 3q93 3whw 3zr0 3zr1 4c9w 4c9x 4n1t 5ans 5ant 5anu 5anv 5anw 5fsi 5fsk 5fsl 5fsm 5fsn 5fso 5ghi 5ghj 5ghm 5ghn 5gho 5ghp 5ghq 5ws7

(-) Related Entries Specified in the PDB File

3zr0 APO MTH1
3zr1 MTH1 IN COMPLEX WITH 8-OXO-DGMP
4n1t MTH1 IN COMPLEX WITH TH287