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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

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

Molecule 1 - DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
	Chains	:	A, B, C, D
	EC Number	:	3.1.5.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA 2
	Expression System Vector	:	PET28
	Expression System Vector Type	:	PLASMID
	Fragment	:	HD DOMAIN, RESIDUES 113-626
	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, SAMHD1

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 20)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	MN	4	Ligand/Ion	MANGANESE (II) ION
3	T8T	12	Ligand/Ion	2'-DEOXYGUANOSINE-5'-O-(1-THIOTRIPHOSPHATE)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN 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:2011	BINDING SITE FOR RESIDUE T8T A 700
02	AC2	SOFTWARE	HIS A:167 , HIS A:206 , ASP A:207 , ASP A:311 , T8T A:700	BINDING SITE FOR RESIDUE MN A 750
03	AC3	SOFTWARE	VAL 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:125	BINDING SITE FOR RESIDUE T8T A 800
04	AC4	SOFTWARE	TYR 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:165	BINDING SITE FOR RESIDUE T8T A 900
05	AC5	SOFTWARE	T8T A:800 , T8T A:900 , HOH A:2012 , LYS D:116	BINDING SITE FOR RESIDUE MG A 950
06	AC6	SOFTWARE	GLN 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:375	BINDING SITE FOR RESIDUE T8T B 700
07	AC7	SOFTWARE	HIS B:167 , HIS B:206 , ASP B:207 , ASP B:311	BINDING SITE FOR RESIDUE MN B 750
08	AC8	SOFTWARE	VAL 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:523	BINDING SITE FOR RESIDUE T8T B 800
09	AC9	SOFTWARE	TYR 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:523	BINDING SITE FOR RESIDUE T8T B 900
10	BC1	SOFTWARE	T8T B:800 , T8T B:900 , LYS C:116	BINDING SITE FOR RESIDUE MG B 950
11	BC2	SOFTWARE	GLN 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:750	BINDING SITE FOR RESIDUE T8T C 700
12	BC3	SOFTWARE	HIS C:167 , HIS C:206 , ASP C:207 , ASP C:311 , T8T C:700	BINDING SITE FOR RESIDUE MN C 750
13	BC4	SOFTWARE	ASP 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:950	BINDING SITE FOR RESIDUE T8T C 800
14	BC5	SOFTWARE	LYS 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:950	BINDING SITE FOR RESIDUE T8T C 900
15	BC6	SOFTWARE	LYS A:523 , LYS B:116 , T8T C:800 , T8T C:900	BINDING SITE FOR RESIDUE MG C 950
16	BC7	SOFTWARE	GLN 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:750	BINDING SITE FOR RESIDUE T8T D 700
17	BC8	SOFTWARE	HIS D:167 , HIS D:206 , ASP D:207 , ASP D:311 , T8T D:700	BINDING SITE FOR RESIDUE MN D 750
18	BC9	SOFTWARE	VAL 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:950	BINDING SITE FOR RESIDUE T8T D 800
19	CC1	SOFTWARE	LYS 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:950	BINDING SITE FOR RESIDUE T8T D 900
20	CC2	SOFTWARE	LYS A:116 , T8T D:800 , T8T D:900	BINDING SITE FOR RESIDUE MG D 950

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

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

Asymmetric/Biological Unit (12, 48)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_058481	H	123	P	SAMH1_HUMAN	Disease (AGS5)	121434520	A/B/C/D	H	123	P
02	UniProt	VAR_058482	R	143	C	SAMH1_HUMAN	Disease (AGS5)	387906948	A/B/C/D	R	143	C
03	UniProt	VAR_058483	R	143	H	SAMH1_HUMAN	Disease (AGS5)	369035155	A/B/C/D	R	143	H
04	UniProt	VAR_058484	R	145	Q	SAMH1_HUMAN	Disease (AGS5)	515726145	A/B/C/D	R	145	Q
05	UniProt	VAR_070633	H	167	Y	SAMH1_HUMAN	Disease (AGS5)	---	A/B/C/D	H	167	Y
06	UniProt	VAR_058485	I	201	N	SAMH1_HUMAN	Disease (CHBL2)	138603088	A/B/C/D	I	201	N
07	UniProt	VAR_058486	G	209	S	SAMH1_HUMAN	Disease (AGS5)	121434516	A/B/C/D	G	209	S
08	UniProt	VAR_058487	M	254	V	SAMH1_HUMAN	Disease (AGS5)	121434521	A/B/C/D	M	254	V
09	UniProt	VAR_070634	R	290	H	SAMH1_HUMAN	Disease (AGS5)	559553527	A/B/C/D	R	290	H
10	UniProt	VAR_058488	L	369	S	SAMH1_HUMAN	Disease (AGS5)	515726139	A/B/C/D	L	369	S
11	UniProt	VAR_058489	M	385	V	SAMH1_HUMAN	Disease (AGS5)	515726140	A/B/C/D	M	385	V
12	UniProt	VAR_078240	I	448	T	SAMH1_HUMAN	Disease (AGS5)	774964432	A/B/C/D	I	448	T

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HD	PS51831	HD domain profile.	SAMH1_HUMAN	164-316	4	A:164-316 B:164-316 C:164-316 D:164-316

Asymmetric/Biological Unit (14, 56)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000262878	1a	ENSE00001898623	chr20:35580246-35579839	408	SAMH1_HUMAN	1-70	70	0	-	-
1.2	ENST00000262878	2	ENSE00001678776	chr20:35575207-35575141	67	SAMH1_HUMAN	70-92	23	0	-	-
1.3	ENST00000262878	3	ENSE00001650543	chr20:35569514-35569442	73	SAMH1_HUMAN	92-116	25	4	A:114-116 B:113-116 C:113-116 D:113-116	3 4 4 4
1.4	ENST00000262878	4	ENSE00001681376	chr20:35563592-35563432	161	SAMH1_HUMAN	117-170	54	4	A:117-170 B:117-170 C:117-170 D:117-170	54 54 54 54
1.5	ENST00000262878	5	ENSE00001594973	chr20:35559278-35559163	116	SAMH1_HUMAN	170-209	40	4	A:170-209 B:170-209 C:170-209 D:170-209	40 40 40 40
1.6	ENST00000262878	6	ENSE00001630356	chr20:35555655-35555585	71	SAMH1_HUMAN	209-232	24	4	A:209-232 B:209-232 C:209-232 D:209-232	24 24 24 24
1.7	ENST00000262878	7	ENSE00001752622	chr20:35547922-35547767	156	SAMH1_HUMAN	233-284	52	4	A:233-284 (gaps) B:233-276 C:233-284 (gaps) D:233-284 (gaps)	52 44 52 52
1.8	ENST00000262878	8	ENSE00001667406	chr20:35545452-35545352	101	SAMH1_HUMAN	285-318	34	4	A:285-318 B:285-318 C:285-318 D:285-318	34 34 34 34
1.9	ENST00000262878	9	ENSE00001793017	chr20:35545233-35545125	109	SAMH1_HUMAN	318-354	37	4	A:318-354 B:318-354 C:318-354 D:318-354	37 37 37 37
1.10	ENST00000262878	10	ENSE00001711142	chr20:35540955-35540864	92	SAMH1_HUMAN	355-385	31	4	A:355-385 B:355-385 C:355-385 D:355-385	31 31 31 31
1.11	ENST00000262878	11	ENSE00001622813	chr20:35539736-35539621	116	SAMH1_HUMAN	385-424	40	4	A:385-424 B:385-424 C:385-424 D:385-424	40 40 40 40
1.12a	ENST00000262878	12a	ENSE00000661815	chr20:35533906-35533767	140	SAMH1_HUMAN	424-470	47	4	A:424-465 B:424-470 C:424-470 D:424-462	42 47 47 39
1.13	ENST00000262878	13	ENSE00000661814	chr20:35532652-35532560	93	SAMH1_HUMAN	471-501	31	4	A:472-501 B:473-501 C:471-501 D:473-501	30 29 31 29
1.14	ENST00000262878	14	ENSE00000661813	chr20:35526947-35526843	105	SAMH1_HUMAN	502-536	35	4	A:502-536 B:502-536 C:502-536 D:502-536	35 35 35 35
1.15a	ENST00000262878	15a	ENSE00000661812	chr20:35526362-35526225	138	SAMH1_HUMAN	537-582	46	4	A:537-582 B:537-582 C:537-582 D:537-582	46 46 46 46
1.16	ENST00000262878	16	ENSE00000800455	chr20:35521469-35518632	2838	SAMH1_HUMAN	583-626	44	4	A:583-599 B:583-599 C:583-599 D:583-599	17 17 17 17

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)
		→ 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 '\|'

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

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

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

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	4bzc
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4bzb	CRYSTAL STRUCTURE OF THE TETRAMERIC DGTP-BOUND SAMHD1 MUTANT CATALYTIC CORE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (12, 48)

PROSITE Motifs (1, 4)

Exons (14, 56)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (23, 23)

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Related Entries Specified in the PDB File