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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TETRAMERIC DGTP-BOUND WILD TYPE SAMHD1 CATALYTIC CORE
 
Authors :  X. Ji, H. Yang, Y. Wu, J. Yan, J. Mehrens, M. Delucia, C. Hao, A. M. Gronenb J. Skowronski, J. Ahn, Y. Xiong
Date :  25 Jul 13  (Deposition) - 23 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.88
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Hiv Restriction Factor, Dntpase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Ji, Y. Wu, J. Yan, J. Mehrens, H. Yang, M. Delucia, C. Hao, A. M. Gronenborn, J. Skowronski, J. Ahn, Y. Xiong
Mechanism Of Allosteric Activation Of Samhd1 By Dgtp
Nat. Struct. Mol. Biol. V. 20 1304 2013
PubMed-ID: 24141705  |  Reference-DOI: 10.1038/NSMB.2692

(-) Compounds

Molecule 1 - DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
    ChainsA, B, C, D
    EC Number3.1.5.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA 2
    Expression System VectorPET28
    Expression System Vector TypePLASMID
    FragmentHD DOMAIN, RESIDUES 113-626
    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

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2MN4Ligand/IonMANGANESE (II) ION
3T8T12Ligand/Ion2'-DEOXYGUANOSINE-5'-O-(1-THIOTRIPHOSPHATE)

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:149 , LEU A:150 , ARG A:164 , ASP A:207 , HIS A:210 , HIS A:215 , HIS A:233 , ASP A:311 , LYS A:312 , TYR A:315 , ASP A:319 , ARG A:366 , HIS A:370 , TYR A:374 , GLN A:375 , MN A:750 , HOH A:2007 , HOH A:2011BINDING SITE FOR RESIDUE T8T A 700
02AC2SOFTWAREHIS A:167 , HIS A:206 , ASP A:207 , ASP A:311 , T8T A:700BINDING SITE FOR RESIDUE MN A 750
03AC3SOFTWAREVAL A:156 , PHE A:157 , GLY A:324 , ARG A:372 , HIS A:376 , LYS A:377 , T8T A:900 , MG A:950 , HOH A:2012 , HOH A:2013 , ARG C:333 , PHE C:337 , ARG C:352 , LYS C:354 , ASN C:358 , LYS C:523 , VAL D:117 , ASN D:119 , HIS D:125BINDING SITE FOR RESIDUE T8T A 800
04AC4SOFTWARETYR A:155 , VAL A:156 , LYS A:377 , VAL A:378 , ARG A:451 , T8T A:800 , MG A:950 , HOH A:2012 , HOH A:2014 , LYS C:523 , LYS D:116 , VAL D:117 , ILE D:118 , ASP D:137 , GLN D:142 , ARG D:145 , PHE D:165BINDING SITE FOR RESIDUE T8T A 900
05AC5SOFTWARET8T A:800 , T8T A:900 , HOH A:2012 , LYS D:116BINDING SITE FOR RESIDUE MG A 950
06AC6SOFTWAREGLN B:149 , LEU B:150 , ARG B:164 , ASP B:207 , HIS B:210 , HIS B:215 , HIS B:233 , ASP B:311 , LYS B:312 , TYR B:315 , ASP B:319 , ARG B:366 , HIS B:370 , TYR B:374 , GLN B:375BINDING SITE FOR RESIDUE T8T B 700
07AC7SOFTWAREHIS B:167 , HIS B:206 , ASP B:207 , ASP B:311BINDING SITE FOR RESIDUE MN B 750
08AC8SOFTWAREVAL B:156 , PHE B:157 , GLY B:324 , ILE B:325 , ARG B:372 , HIS B:376 , LYS B:377 , T8T B:900 , MG B:950 , HOH B:2009 , VAL C:117 , ASN C:119 , ARG D:333 , PHE D:337 , ARG D:352 , LYS D:354 , ASN D:358 , LYS D:523BINDING SITE FOR RESIDUE T8T B 800
09AC9SOFTWARETYR B:155 , VAL B:156 , VAL B:378 , ARG B:451 , LYS B:455 , T8T B:800 , MG B:950 , HOH B:2007 , LYS C:116 , VAL C:117 , ILE C:118 , ASP C:137 , GLN C:142 , ARG C:145 , PHE C:165 , LYS D:523BINDING SITE FOR RESIDUE T8T B 900
10BC1SOFTWARET8T B:800 , T8T B:900 , LYS C:116BINDING SITE FOR RESIDUE MG B 950
11BC2SOFTWAREGLN C:149 , LEU C:150 , ARG C:164 , ASP C:207 , HIS C:210 , HIS C:215 , HIS C:233 , ASP C:311 , LYS C:312 , TYR C:315 , ASP C:319 , ARG C:366 , TYR C:374 , GLN C:375 , MN C:750BINDING SITE FOR RESIDUE T8T C 700
12BC3SOFTWAREHIS C:167 , HIS C:206 , ASP C:207 , ASP C:311 , T8T C:700BINDING SITE FOR RESIDUE MN C 750
13BC4SOFTWAREASP A:330 , ARG A:333 , PHE A:337 , ARG A:352 , LYS A:354 , ASN A:358 , LYS A:523 , VAL B:117 , ASN B:119 , VAL C:156 , PHE C:157 , GLY C:324 , ILE C:325 , ARG C:372 , HIS C:376 , LYS C:377 , T8T C:900 , MG C:950BINDING SITE FOR RESIDUE T8T C 800
14BC5SOFTWARELYS A:523 , LYS B:116 , VAL B:117 , ILE B:118 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165 , TYR C:155 , VAL C:156 , VAL C:378 , ARG C:451 , LYS C:455 , T8T C:800 , MG C:950BINDING SITE FOR RESIDUE T8T C 900
15BC6SOFTWARELYS A:523 , LYS B:116 , T8T C:800 , T8T C:900BINDING SITE FOR RESIDUE MG C 950
16BC7SOFTWAREGLN D:149 , LEU D:150 , ARG D:164 , ASP D:207 , HIS D:210 , HIS D:215 , HIS D:233 , ASP D:311 , LYS D:312 , TYR D:315 , ASP D:319 , TYR D:374 , GLN D:375 , MN D:750BINDING SITE FOR RESIDUE T8T D 700
17BC8SOFTWAREHIS D:167 , HIS D:206 , ASP D:207 , ASP D:311 , T8T D:700BINDING SITE FOR RESIDUE MN D 750
18BC9SOFTWAREVAL A:117 , ASN A:119 , ASP B:330 , ARG B:333 , PHE B:337 , ARG B:352 , LYS B:354 , LYS B:523 , VAL D:156 , PHE D:157 , GLY D:324 , ILE D:325 , ARG D:372 , HIS D:376 , LYS D:377 , T8T D:900 , MG D:950BINDING SITE FOR RESIDUE T8T D 800
19CC1SOFTWARELYS A:116 , VAL A:117 , ILE A:118 , ASP A:137 , GLN A:142 , ARG A:145 , PHE A:165 , LYS B:523 , TYR D:155 , VAL D:156 , LYS D:377 , VAL D:378 , ARG D:451 , T8T D:800 , MG D:950BINDING SITE FOR RESIDUE T8T D 900
20CC2SOFTWARELYS A:116 , T8T D:800 , T8T D:900BINDING SITE FOR RESIDUE MG D 950

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (12, 48)

Asymmetric/Biological Unit (12, 48)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_058481H123PSAMH1_HUMANDisease (AGS5)121434520A/B/C/DH123P
02UniProtVAR_058482R143CSAMH1_HUMANDisease (AGS5)387906948A/B/C/DR143C
03UniProtVAR_058483R143HSAMH1_HUMANDisease (AGS5)369035155A/B/C/DR143H
04UniProtVAR_058484R145QSAMH1_HUMANDisease (AGS5)515726145A/B/C/DR145Q
05UniProtVAR_070633H167YSAMH1_HUMANDisease (AGS5)  ---A/B/C/DH167Y
06UniProtVAR_058485I201NSAMH1_HUMANDisease (CHBL2)138603088A/B/C/DI201N
07UniProtVAR_058486G209SSAMH1_HUMANDisease (AGS5)121434516A/B/C/DG209S
08UniProtVAR_058487M254VSAMH1_HUMANDisease (AGS5)121434521A/B/C/DM254V
09UniProtVAR_070634R290HSAMH1_HUMANDisease (AGS5)559553527A/B/C/DR290H
10UniProtVAR_058488L369SSAMH1_HUMANDisease (AGS5)515726139A/B/C/DL369S
11UniProtVAR_058489M385VSAMH1_HUMANDisease (AGS5)515726140A/B/C/DM385V
12UniProtVAR_078240I448TSAMH1_HUMANDisease (AGS5)774964432A/B/C/DI448T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HDPS51831 HD domain profile.SAMH1_HUMAN164-316
 
 
 
  4A:164-316
B:164-316
C:164-316
D:164-316

(-) Exons   (14, 56)

Asymmetric/Biological Unit (14, 56)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002628781aENSE00001898623chr20:35580246-35579839408SAMH1_HUMAN1-70700--
1.2ENST000002628782ENSE00001678776chr20:35575207-3557514167SAMH1_HUMAN70-92230--
1.3ENST000002628783ENSE00001650543chr20:35569514-3556944273SAMH1_HUMAN92-116254A:114-116
B:113-116
C:113-116
D:113-116
3
4
4
4
1.4ENST000002628784ENSE00001681376chr20:35563592-35563432161SAMH1_HUMAN117-170544A:117-170
B:117-170
C:117-170
D:117-170
54
54
54
54
1.5ENST000002628785ENSE00001594973chr20:35559278-35559163116SAMH1_HUMAN170-209404A:170-209
B:170-209
C:170-209
D:170-209
40
40
40
40
1.6ENST000002628786ENSE00001630356chr20:35555655-3555558571SAMH1_HUMAN209-232244A:209-232
B:209-232
C:209-232
D:209-232
24
24
24
24
1.7ENST000002628787ENSE00001752622chr20:35547922-35547767156SAMH1_HUMAN233-284524A:233-284 (gaps)
B:233-276
C:233-284 (gaps)
D:233-284 (gaps)
52
44
52
52
1.8ENST000002628788ENSE00001667406chr20:35545452-35545352101SAMH1_HUMAN285-318344A:285-318
B:285-318
C:285-318
D:285-318
34
34
34
34
1.9ENST000002628789ENSE00001793017chr20:35545233-35545125109SAMH1_HUMAN318-354374A:318-354
B:318-354
C:318-354
D:318-354
37
37
37
37
1.10ENST0000026287810ENSE00001711142chr20:35540955-3554086492SAMH1_HUMAN355-385314A:355-385
B:355-385
C:355-385
D:355-385
31
31
31
31
1.11ENST0000026287811ENSE00001622813chr20:35539736-35539621116SAMH1_HUMAN385-424404A:385-424
B:385-424
C:385-424
D:385-424
40
40
40
40
1.12aENST0000026287812aENSE00000661815chr20:35533906-35533767140SAMH1_HUMAN424-470474A:424-465
B:424-470
C:424-470
D:424-462
42
47
47
39
1.13ENST0000026287813ENSE00000661814chr20:35532652-3553256093SAMH1_HUMAN471-501314A:472-501
B:473-501
C:471-501
D:473-501
30
29
31
29
1.14ENST0000026287814ENSE00000661813chr20:35526947-35526843105SAMH1_HUMAN502-536354A:502-536
B:502-536
C:502-536
D:502-536
35
35
35
35
1.15aENST0000026287815aENSE00000661812chr20:35526362-35526225138SAMH1_HUMAN537-582464A:537-582
B:537-582
C:537-582
D:537-582
46
46
46
46
1.16ENST0000026287816ENSE00000800455chr20:35521469-355186322838SAMH1_HUMAN583-626444A:583-599
B:583-599
C:583-599
D:583-599
17
17
17
17

(-) Sequences/Alignments

Asymmetric/Biological 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:476
 aligned with SAMH1_HUMAN | Q9Y3Z3 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:486
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593      
          SAMH1_HUMAN   114 TMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLESPVEDSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
               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..hhhhhhhhhhhhhhhh....eeeeee.....------..hhhhhhhhhh..........hhh.eeeeeeeee......hhhhhh.eee..eeeeee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhh.... Sec.struct. author
             SAPs(SNPs) (1) ---------P-------------------C-Q---------------------Y---------------------------------N-------S--------------------------------------------V-----------------------------------H------------------------------------------------------------------------------S---------------V--------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------HD  PDB: A:164-316 UniProt: 164-316                                                                                                                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.3Exon 1.4  PDB: A:117-170 UniProt: 117-170             --------------------------------------Exon 1.6  PDB: A:209-232Exon 1.7  PDB: A:233-284 (gaps) UniProt: 233-284    Exon 1.8  PDB: A:285-318          ------------------------------------Exon 1.10  PDB: A:355-385      --------------------------------------Exon 1.12a  PDB: A:424-465 UniProt: 424-470    Exon 1.13  PDB: A:472-501      Exon 1.14  PDB: A:502-536          Exon 1.15a  PDB: A:537-582 UniProt: 537-582   Exon 1.16         Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.5  PDB: A:170-209                ------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:318-354             ------------------------------Exon 1.11  PDB: A:385-424               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 4bzc A 114 TMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLE----DSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQ------DYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273   |   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463 |     473       483       493       503       513       523       533       543       553       563       573       583       593      
                                                                                                                                                                                             277  282                                                                                                                                                                                    465    472                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:477
 aligned with SAMH1_HUMAN | Q9Y3Z3 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:487
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       
          SAMH1_HUMAN   113 DTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLESPVEDSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
               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..hhhhhhhhhh.hhhhhhhhhhhhhhhh....eeeeee..........--..hhhhhhhhh..........hhh.eeeeeeeee......hhhhhh.eee..eeeeee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhh.... Sec.struct. author
             SAPs(SNPs) (1) ----------P-------------------C-Q---------------------Y---------------------------------N-------S--------------------------------------------V-----------------------------------H------------------------------------------------------------------------------S---------------V--------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------HD  PDB: B:164-316 UniProt: 164-316                                                                                                                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.3 Exon 1.4  PDB: B:117-170 UniProt: 117-170             --------------------------------------Exon 1.6  PDB: B:209-232Exon 1.7  PDB: B:233-276 UniProt: 233-284           Exon 1.8  PDB: B:285-318          ------------------------------------Exon 1.10  PDB: B:355-385      --------------------------------------Exon 1.12a  PDB: B:424-470 UniProt: 424-470    Exon 1.13  PDB: B:473-501      Exon 1.14  PDB: B:502-536          Exon 1.15a  PDB: B:537-582 UniProt: 537-582   Exon 1.16         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.5  PDB: B:170-209                ------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: B:318-354             ------------------------------Exon 1.11  PDB: B:385-424               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 4bzc B 113 DTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPL--------WPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKR--YESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   |     -  |    292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       | -|      482       492       502       512       522       532       542       552       562       572       582       592       
                                                                                                                                                                                             276      285                                                                                                                                                                                      470  |                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                  473                                                                                                                              

Chain C from PDB  Type:PROTEIN  Length:481
 aligned with SAMH1_HUMAN | Q9Y3Z3 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:487
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       
          SAMH1_HUMAN   113 DTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLESPVEDSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
               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..hhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhh..........hhh.eeeeeeeee......hhhhhh.eee..eeeeee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhh.... Sec.struct. author
             SAPs(SNPs) (1) ----------P-------------------C-Q---------------------Y---------------------------------N-------S--------------------------------------------V-----------------------------------H------------------------------------------------------------------------------S---------------V--------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------HD  PDB: C:164-316 UniProt: 164-316                                                                                                                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.3 Exon 1.4  PDB: C:117-170 UniProt: 117-170             --------------------------------------Exon 1.6  PDB: C:209-232Exon 1.7  PDB: C:233-284 (gaps) UniProt: 233-284    Exon 1.8  PDB: C:285-318          ------------------------------------Exon 1.10  PDB: C:355-385      --------------------------------------Exon 1.12a  PDB: C:424-470 UniProt: 424-470    Exon 1.13  PDB: C:471-501      Exon 1.14  PDB: C:502-536          Exon 1.15a  PDB: C:537-582 UniProt: 537-582   Exon 1.16         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.5  PDB: C:170-209                ------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: C:318-354             ------------------------------Exon 1.11  PDB: C:385-424               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 4bzc C 113 DTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLE------LWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    |    - |     292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       
                                                                                                                                                                                              277    284                                                                                                                                                                                                                                                                                                                           

Chain D from PDB  Type:PROTEIN  Length:470
 aligned with SAMH1_HUMAN | Q9Y3Z3 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:487
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       
          SAMH1_HUMAN   113 DTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPLESPVEDSLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKREDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
               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..hhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee..----------..hhhhhhhhh..........hhh.eeeeeeeee......hhhhhheeee..eeeeee..hhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhh.... Sec.struct. author
             SAPs(SNPs) (1) ----------P-------------------C-Q---------------------Y---------------------------------N-------S--------------------------------------------V-----------------------------------H------------------------------------------------------------------------------S---------------V--------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------HD  PDB: D:164-316 UniProt: 164-316                                                                                                                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.3 Exon 1.4  PDB: D:117-170 UniProt: 117-170             --------------------------------------Exon 1.6  PDB: D:209-232Exon 1.7  PDB: D:233-284 (gaps) UniProt: 233-284    Exon 1.8  PDB: D:285-318          ------------------------------------Exon 1.10  PDB: D:355-385      --------------------------------------Exon 1.12a  PDB: D:424-462 UniProt: 424-470    Exon 1.13  PDB: D:473-501      Exon 1.14  PDB: D:502-536          Exon 1.15a  PDB: D:537-582 UniProt: 537-582   Exon 1.16         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.5  PDB: D:170-209                ------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: D:318-354             ------------------------------Exon 1.11  PDB: D:385-424               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 4bzc D 113 DTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASHNRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEEDICFIKEQIVGPL-------LWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQP----------YESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNFTKPQDGDVIAPLITPQKKEWN 599
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   |     - |     292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462         -|      482       492       502       512       522       532       542       552       562       572       582       592       
                                                                                                                                                                                             276     284                                                                                                                                                                               462        473                                                                                                                              

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4BZC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SAMH1_HUMAN | Q9Y3Z3)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0032567    dGTP binding    Interacting selectively and non-covalently with dGTP, deoxyguanosine triphosphate.
    GO:0008832    dGTPase activity    Catalysis of the reaction: dGTP + H(2)O = 2'-deoxyguanosine + 2 H(+) + triphosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0046061    dATP catabolic process    The chemical reactions and pathways resulting in the breakdown of dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate).
    GO:0006203    dGTP catabolic process    The chemical reactions and pathways resulting in the breakdown of dGTP, guanosine triphosphate.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0045088    regulation of innate immune response    Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0060337    type I interferon signaling pathway    A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SAMH1_HUMAN | Q9Y3Z32e8o 3u1n 4bzb 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 5ao0 5ao1 5ao2 5ao3 5ao4

(-) Related Entries Specified in the PDB File

4bzb CRYSTAL STRUCTURE OF THE TETRAMERIC DGTP-BOUND SAMHD1 MUTANT CATALYTIC CORE