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(-) Description

Title :  THE STRUCTURE OF GTP-BOUND SAMHD1
 
Authors :  C. F. Zhu, W. Wei, X. Peng, Y. H. Dong, Y. Gong, X. F. Yu
Date :  11 Dec 14  (Deposition) - 11 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hd-Domain, Hydrolase, Dntp And Gtp Binding, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. F. Zhu, W. Wei, X. Peng, Y. H. Dong, Y. Gong, X. F. Yu
The Mechanism Of Substrate-Controlled Allosteric Regulation Of Samhd1 Activated By Gtp.
Acta Crystallogr. , Sect. D V. 71 516 2015
PubMed-ID: 25760601  |  Reference-DOI: 10.1107/S1399004714027527

(-) Compounds

Molecule 1 - DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
    Chains: A, B, C, D
    EC Number: 3.1.5.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SAMHD1, MOP5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNTPASE, DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN, DCIP, MONOCYTE PROTEIN 5, MOP-5, SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2PO44Ligand/IonPHOSPHATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2PO42Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2PO42Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:164 , HIS A:167 , HIS A:206 , ASP A:207 , ASP A:311 , PO4 A:702BINDING SITE FOR RESIDUE ZN A 701
02AC2SOFTWAREARG A:164 , HIS A:167 , ASP A:207 , HIS A:210 , HIS A:215 , HIS A:233 , ASP A:311 , TYR A:315 , ZN A:701 , HOH A:847BINDING SITE FOR RESIDUE PO4 A 702
03AC3SOFTWARETYR A:155 , VAL A:156 , VAL A:378 , ARG A:451 , LEU A:453 , LYS B:116 , VAL B:117 , ILE B:118 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165 , HOH B:972BINDING SITE FOR RESIDUE GTP B 801
04AC4SOFTWAREHIS B:167 , HIS B:206 , ASP B:207 , ASP B:311 , PO4 B:804BINDING SITE FOR RESIDUE ZN B 802
05AC5SOFTWARELYS A:116 , VAL A:117 , ILE A:118 , ASP A:137 , GLN A:142 , ARG A:145 , PHE A:165 , TYR B:155 , VAL B:156 , ARG B:451 , LEU B:453 , LYS B:455 , HOH B:936 , HOH B:975BINDING SITE FOR RESIDUE GTP B 803
06AC6SOFTWAREARG B:164 , HIS B:167 , ASP B:207 , HIS B:210 , HIS B:215 , HIS B:233 , ASP B:311 , ZN B:802 , HOH B:930BINDING SITE FOR RESIDUE PO4 B 804
07AC7SOFTWAREARG C:164 , HIS C:167 , HIS C:206 , ASP C:207 , ASP C:311 , PO4 C:703BINDING SITE FOR RESIDUE ZN C 701
08AC8SOFTWARETYR C:155 , VAL C:156 , VAL C:378 , ARG C:451 , HOH C:830 , HOH C:856 , HOH C:857 , HOH C:861 , LYS D:116 , VAL D:117 , ILE D:118 , ASP D:137 , GLN D:142 , ARG D:145 , PHE D:165 , HOH D:834BINDING SITE FOR RESIDUE GTP C 702
09AC9SOFTWAREARG C:164 , HIS C:167 , ASP C:207 , HIS C:210 , HIS C:215 , HIS C:233 , ASP C:311 , ZN C:701 , HOH C:863BINDING SITE FOR RESIDUE PO4 C 703
10BC1SOFTWAREHIS D:167 , HIS D:206 , ASP D:207 , ASP D:311 , PO4 D:703BINDING SITE FOR RESIDUE ZN D 701
11BC2SOFTWARELYS C:116 , VAL C:117 , ILE C:118 , ASP C:137 , GLN C:142 , ARG C:145 , PHE C:165 , TYR D:155 , VAL D:156 , VAL D:378 , ARG D:451 , LEU D:453BINDING SITE FOR RESIDUE GTP D 702
12BC3SOFTWAREARG D:164 , HIS D:167 , ASP D:207 , HIS D:210 , HIS D:215 , HIS D:233 , ASP D:311 , ZN D:701 , HOH D:846BINDING SITE FOR RESIDUE PO4 D 703

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:341 -A:350
2B:341 -B:350
3C:341 -C:350
4D:341 -D:350

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RXO)

(-) 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:456
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeee........hhhhhh.ee..................eeeeeee...hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rxo A 114 TMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLELWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRILPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQD 583
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273   ||  289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529  ||   547       557       567       577      
                                                                                                                                                                                             277|                                                                                                                                                                                                                                                     532|                                          
                                                                                                                                                                                              284                                                                                                                                                                                                                                                      541                                          


Chain B from PDB  Type:PROTEIN  Length:433
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeee.....ee....eeeeeee...hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rxo B 114 TMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLESLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDHVSFYKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQD 583
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273   ||  288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498      |518  ||   550       560       570       580   
                                                                                                                                                                                             277|                                                                                                                                                                                                                           505|  521|                                       
                                                                                                                                                                                              283                                                                                                                                                                                                                            516   544                                       


Chain C from PDB  Type:PROTEIN  Length:434
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh............hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeee......ee...eeeeeee...hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rxo C 114 TMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLESSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMIDHVSFYCKEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQD 583
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273    || 287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       516      |549       559       569       579    
                                                                                                                                                                                              278|                                                                                                                                                                                                                           505|     523|                                    
                                                                                                                                                                                               283                                                                                                                                                                                                                            515      547                                    


Chain D from PDB  Type:PROTEIN  Length:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeee........ee.............eeeeeee...hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rxo D 114 TMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLELWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYIDHVSFYCKTAPNRAIRIAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQD 583
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273   ||  289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       516       526     ||549       559       569       579    
                                                                                                                                                                                             277|                                                                                                                                                                                                                            507|              532|                                     
                                                                                                                                                                                              284                                                                                                                                                                                                                             515               546
   Legend:   → Mismatch (orange background)
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  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 4RXO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

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  SAMH1_HUMAN | Q9Y3Z3
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 Related Entries

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UniProtKB/Swiss-Prot
        SAMH1_HUMAN | Q9Y3Z3: 2e8o 3u1n 4bzb 4bzc 4cc9 4mz7 4q7h 4qfx 4qfy 4qfz 4qg0 4qg1 4qg2 4qg4 4rxp 4rxq 4rxr 4rxs 4tnp 4tnq 4tnr 4tnx 4tny 4tnz 4to0 4to1 4to2 4to3 4to4 4to5 4to6 4zwe 4zwg 5ao0 5ao1 5ao2 5ao3 5ao4

(-) Related Entries Specified in the PDB File

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