Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF GTP-DCTP-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 :  2.12
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
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
    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

  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
1DCP4Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1DCP8Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:149 , LEU A:150 , ARG A:164 , HIS A:215 , LYS A:312 , TYR A:315 , ASP A:319 , ARG A:366 , HIS A:370 , TYR A:374 , GLN A:375 , HOH A:822 , HOH A:829 , HOH A:832 , HOH A:835BINDING SITE FOR RESIDUE DCP A 701
2AC2SOFTWARELYS A:116 , GTP B:801 , DCP B:802 , HOH B:924BINDING SITE FOR RESIDUE MG A 702
3AC3SOFTWAREVAL A:156 , PHE A:157 , ARG A:333 , PHE A:337 , ARG A:352 , LYS A:354 , ASN A:358 , ARG A:372 , HIS A:376 , LYS A:377 , VAL A:378 , LYS A:523 , HOH A:814 , HOH A:915 , HOH A:917 , HOH A:926 , HOH A:982 , VAL B:117 , ASN B:119 , GTP B:803 , MG B:805 , HOH B:933BINDING SITE FOR RESIDUE DCP A 703
4AC4SOFTWARELYS A:116 , VAL A:117 , ILE A:118 , ASP A:137 , GLN A:142 , ARG A:145 , PHE A:165 , MG A:702 , TYR B:155 , VAL B:156 , VAL B:378 , ARG B:451 , LYS B:523 , DCP B:802 , HOH B:924 , HOH B:936 , HOH B:939 , HOH B:971 , HOH B:1013BINDING SITE FOR RESIDUE GTP B 801
5AC5SOFTWAREVAL A:117 , ILE A:118 , ASN A:119 , MG A:702 , VAL B:156 , PHE B:157 , ARG B:333 , PHE B:337 , ARG B:352 , LYS B:354 , ASN B:358 , ARG B:372 , HIS B:376 , LYS B:377 , VAL B:378 , LYS B:523 , GTP B:801 , HOH B:921 , HOH B:924 , HOH B:1018 , HOH B:1067BINDING SITE FOR RESIDUE DCP B 802
6AC6SOFTWARETYR A:155 , VAL A:156 , VAL A:378 , ARG A:451 , LYS A:523 , DCP A:703 , HOH A:874 , LYS B:116 , VAL B:117 , ILE B:118 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165 , MG B:805 , HOH B:933 , HOH B:946 , HOH B:1034 , HOH B:1038 , HOH B:1065BINDING SITE FOR RESIDUE GTP B 803
7AC7SOFTWAREGLN B:149 , LEU B:150 , ARG B:164 , HIS B:215 , GLU B:234 , LYS B:312 , TYR B:315 , ASP B:319 , ARG B:366 , HIS B:370 , TYR B:374 , GLN B:375 , HOH B:903 , HOH B:909 , HOH B:932 , HOH B:954BINDING SITE FOR RESIDUE DCP B 804
8AC8SOFTWAREDCP A:703 , LYS B:116 , GTP B:803 , HOH B:933BINDING SITE FOR RESIDUE MG B 805

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RXR)

(-) 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:481
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeeeee......hhhhhheeee..eeeeee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rxr A 114 TMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLESLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
                                   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       508       518       528       538       548       558       568       578       588       598 
                                                                                                                                                                                              278|                                                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                               284                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:493
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee......eeeee...eeeeehhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhheeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....ee.hhh.ee...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhh..........hhh.eeeeeeeee......hhhhhheeee..eeeeee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rxr B 102 NLYFQGSQIHVDTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDIYFIKEQIVGPLESLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      |286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596   
                                                                                                                                                                                                          278|                                                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                           284
   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 4RXR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    DCP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rxr)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4rxr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SAMH1_HUMAN | Q9Y3Z3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.5.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SAMH1_HUMAN | Q9Y3Z3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SAMH1_HUMAN | Q9Y3Z3: 2e8o 3u1n 4bzb 4bzc 4cc9 4mz7 4q7h 4qfx 4qfy 4qfz 4qg0 4qg1 4qg2 4qg4 4rxo 4rxp 4rxq 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

(no "Related Entries Specified in the PDB File" available for 4RXR)