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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 41-583) BOUND TO DDGTP
 
Authors :  D. Schwefel, I. A. Taylor
Date :  09 Sep 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.73
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase, Deoxynucleoside, Deoxynucleoside Triphosphate Triphosphohydrolase, Hiv Restriction Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. H. Arnold, H. C. Groom, S. Kunzelmann, D. Schwefel, S. J. Caswell, P. Ordonez, M. C. Mann, S. Rueschenbaum, D. C. Goldstone, S. Pennell, S. A. Howell, J. P. Stoye, M. Webb, I. A. Taylor, K. N. Bishop
Phospho-Dependent Regulation Of Samhd1 Oligomerisation Couples Catalysis And Restriction.
Plos Pathog. V. 11 05194 2015
PubMed-ID: 26431200  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005194

(-) Compounds

Molecule 1 - DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA PLYSS
    Expression System VectorPET52B
    Expression System Vector TypePLASMID
    FragmentRESIDUES 41-583
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDNTPASE, DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN, DCIP, MONOCYTE PROTEIN 5, MOP-5, SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN 1, SAMHD1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1DG34Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
2FE2Ligand/IonFE (III) ION
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1DG38Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
2FE-1Ligand/IonFE (III) ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:167 , HIS A:206 , ASP A:207 , ASP A:311 , DG3 A:2001BINDING SITE FOR RESIDUE FE A1001
2AC2SOFTWAREARG A:164 , HIS A:167 , HIS A:206 , ASP A:207 , HIS A:210 , HIS A:215 , HIS A:233 , ASP A:311 , LYS A:312 , TYR A:315 , TYR A:374 , ASN A:380 , FE A:1001BINDING SITE FOR RESIDUE DG3 A2001
3AC3SOFTWARELYS A:116 , ILE A:118 , ASP A:137 , GLN A:142 , ARG A:145 , PHE A:165 , MG A:3001 , HOH A:4002 , TYR B:155 , VAL B:156 , VAL B:378 , ARG B:451 , LEU B:453BINDING SITE FOR RESIDUE DG3 A2002
4AC4SOFTWAREDG3 A:2002BINDING SITE FOR RESIDUE MG A3001
5AC5SOFTWAREHIS B:167 , HIS B:206 , ASP B:207 , ASP B:311 , DG3 B:2001BINDING SITE FOR RESIDUE FE B1001
6AC6SOFTWAREARG B:164 , HIS B:167 , HIS B:206 , ASP B:207 , HIS B:210 , HIS B:215 , HIS B:233 , ASP B:311 , TYR B:315 , HIS B:370 , TYR B:374 , ASN B:380 , FE B:1001BINDING SITE FOR RESIDUE DG3 B2001
7AC7SOFTWARETYR A:155 , VAL A:156 , VAL A:378 , ARG A:451 , LEU A:453 , LYS B:116 , VAL B:117 , ILE B:118 , ILE B:136 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165 , MG B:3001 , HOH B:4001BINDING SITE FOR RESIDUE DG3 B2002
8AC8SOFTWAREDG3 B:2002BINDING SITE FOR RESIDUE MG B3001

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:341 -A:350
2B:341 -B:350

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro B:581 -Gln B:582

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AO0)

(-) Exons   (0, 0)

(no "Exon" information available for 5AO0)

(-) 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:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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.....hhhhhhhhheeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeee........hhhhh.hhhhhhhh...........hhh.eeeeeee...eeee..eeeeee..eeeeeee...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ao0 A 110 IHVDTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMHVSFYCKTAPNRAIREQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQ 582
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269      |287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       518       528  ||   553       563       573         
                                                                                                                                                                                                276|                                                                                                                                                                                                                         505|           531|                                   
                                                                                                                                                                                                 285                                                                                                                                                                                                                          517            547                                   

Chain B from PDB  Type:PROTEIN  Length:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               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.....hhhhhhhh.eeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...ee.hhh.ee...hhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeee......hhhhh.hhhhhhhh...........hhh.eeeeee......ee.........eeeeee...hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ao0 B 113 DTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLELWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDHVSFYCKTAPNRAQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQD 583
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    || 288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458    || 470       480       490       500     ||520       548       558       568       578     
                                                                                                                                                                                              277|                                                                                                                                                                                463|                                     506|         529|                                   
                                                                                                                                                                                               284                                                                                                                                                                                 466                                      517          548                                   

   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 5AO0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AO0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AO0)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SAMH1_HUMAN | Q9Y3Z32e8o 3u1n 4bzb 4bzc 4cc9 4mz7 4q7h 4qfx 4qfy 4qfz 4qg0 4qg1 4qg2 4qg4 4rxo 4rxp 4rxq 4rxr 4rxs 4tnp 4tnq 4tnr 4tnx 4tny 4tnz 4to0 4to1 4to2 4to3 4to4 4to5 4to6 4zwe 4zwg 5ao1 5ao2 5ao3 5ao4

(-) Related Entries Specified in the PDB File

5ao1 CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 115-583) BOUND TO DDGTP
5ao2 CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 115-583) R164A VARIANT BOUND TO DGTP
5ao3 CRYSTAL STRUCTURE OF HUMAN SAMHD1 (AMINO ACID RESIDUES 115-626) BOUND TO GTP
5ao4 CRYSTAL STRUCTURE OF IN VITRO PHOSPHORYLATED HUMAN SAMHD1 (AMINO ACID RESIDUES 115-626) BOUND TO GTP