3SE2 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   HUMAN POLY(ADP-RIBOSE) POLYMERASE 14 (PARP14/ARTD8) - CATALYTIC DOMAIN IN COMPLEX WITH 6(5H)-PHENANTHRIDINONE

Authors :   T. Karlberg, P. Schutz, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Co A. M. Edwards, T. Ekblad, S. Graslund, E. Kouznetsova, M. Moche, P. Nor T. Nyman, A. G. Thorsell, L. Tresaugues, J. Weigelt, M. I. Siponen, H. S Structural Genomics Consortium (Sgc)

Date :   10 Jun 11 (Deposition) - 06 Jul 11 (Release) - 21 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A,C  (1x)
Biol. Unit 6: B,D  (1x)

Keywords :   Diphtheria Toxin Like Fold, Transferase, Nad+, Adp-Ribosylation, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Wahlberg, T. Karlberg, E. Kouznetsova, N. Markova, A. Macchiarulo A. G. Thorsell, E. Pol, A. Frostell, T. Ekblad, D. Oncu, B. Kull, G. M. Robertson, R. Pellicciari, H. Schuler, J. Weigelt
Family-Wide Chemical Profiling And Structural Analysis Of Parp And Tankyrase Inhibitors.
Nat. Biotechnol. V. 30 283 2012
PubMed-ID: 22343925 | Reference-DOI: 10.1038/NBT.2121

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 14
	Chains	:	A, B, C, D
	EC Number	:	2.4.2.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3) R3 PRARE
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	BAL2, KIAA1268, PARP14
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PARP-14, B AGGRESSIVE LYMPHOMA PROTEIN 2

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:	A		C
Biological Unit 6 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	3AB	2	Ligand/Ion	3-AMINOBENZAMIDE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	GOL	4	Ligand/Ion	GLYCEROL
4	LDR	2	Ligand/Ion	PHENANTHRIDIN-6(5H)-ONE
5	SCN	3	Ligand/Ion	THIOCYANATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	3AB	-1	Ligand/Ion	3-AMINOBENZAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	LDR	1	Ligand/Ion	PHENANTHRIDIN-6(5H)-ONE
5	SCN	-1	Ligand/Ion	THIOCYANATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	3AB	-1	Ligand/Ion	3-AMINOBENZAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	-1	Ligand/Ion	GLYCEROL
4	LDR	1	Ligand/Ion	PHENANTHRIDIN-6(5H)-ONE
5	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	3AB	1	Ligand/Ion	3-AMINOBENZAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	LDR	-1	Ligand/Ion	PHENANTHRIDIN-6(5H)-ONE
5	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	3AB	1	Ligand/Ion	3-AMINOBENZAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	LDR	-1	Ligand/Ion	PHENANTHRIDIN-6(5H)-ONE
5	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 5 (4, 6)

No.	Name	Count	Type	Full Name
1	3AB	1	Ligand/Ion	3-AMINOBENZAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	3	Ligand/Ion	GLYCEROL
4	LDR	1	Ligand/Ion	PHENANTHRIDIN-6(5H)-ONE
5	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 6 (4, 5)

No.	Name	Count	Type	Full Name
1	3AB	1	Ligand/Ion	3-AMINOBENZAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	LDR	1	Ligand/Ion	PHENANTHRIDIN-6(5H)-ONE
5	SCN	2	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:1601 , GLY A:1602 , LYS A:1623 , ASN A:1624 , ALA A:1625 , TYR A:1633 , TYR A:1640 , SER A:1641 , TYR A:1646	BINDING SITE FOR RESIDUE LDR A 1
02	AC2	SOFTWARE	ASN A:1549 , ALA A:1552 , SER A:1553 , ASN A:1556 , ILE D:1675 , VAL D:1676 , PHE D:1705 , TYR D:1706	BINDING SITE FOR RESIDUE GOL A 1721
03	AC3	SOFTWARE	ILE A:1570 , ASN A:1572 , PRO A:1573 , TYR A:1711	BINDING SITE FOR RESIDUE GOL A 3
04	AC4	SOFTWARE	HIS B:1601 , GLY B:1602 , ALA B:1625 , TYR B:1633 , TYR B:1640 , SER B:1641 , TYR B:1646	BINDING SITE FOR RESIDUE LDR B 2
05	AC5	SOFTWARE	GLN B:1534 , ASN B:1614 , ASN B:1617 , TYR B:1708	BINDING SITE FOR RESIDUE SCN B 5
06	AC6	SOFTWARE	HOH C:130 , HIS C:1601 , GLY C:1602 , TYR C:1633 , ALA C:1635 , SER C:1641 , TYR C:1646	BINDING SITE FOR RESIDUE 3AB C 4
07	AC7	SOFTWARE	ASN C:1612	BINDING SITE FOR RESIDUE CL C 2
08	AC8	SOFTWARE	ARG C:1569 , ILE C:1570 , GLN C:1571 , ASN C:1572 , TYR C:1711 , GLU C:1713	BINDING SITE FOR RESIDUE GOL C 1721
09	AC9	SOFTWARE	LYS B:1582 , TYR B:1706 , ASP B:1707 , PRO C:1543 , SER C:1544	BINDING SITE FOR RESIDUE SCN C 7
10	BC1	SOFTWARE	HIS D:1601 , GLY D:1602 , TYR D:1633 , SER D:1641 , TYR D:1646 , HOH D:1721	BINDING SITE FOR RESIDUE 3AB D 3
11	BC2	SOFTWARE	ASN B:1612	BINDING SITE FOR RESIDUE CL D 1
12	BC3	SOFTWARE	GLN D:1571 , PRO D:1573 , TRP D:1576 , TYR D:1711	BINDING SITE FOR RESIDUE GOL D 4
13	BC4	SOFTWARE	TYR A:1706 , ASP A:1707 , SER D:1544	BINDING SITE FOR RESIDUE SCN D 6

Asymmetric Unit

No.	Residues
1	A:1537	-	C:1537
2	B:1537	-	D:1537

(no "Cis Peptide Bond" information available for 3SE2)

(no "SAP(SNP)/Variant" information available for 3SE2)

(no "PROSITE Motif" information available for 3SE2)

(no "Exon" information available for 3SE2)

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:186
 aligned with PAR14_HUMAN | Q460N5 from UniProtKB/Swiss-Prot  Length:1801

    Alignment length:189
                                  1622      1632      1642      1652      1662      1672      1682      1692      1702      1712      1722      1732      1742      1752      1762      1772      1782      1792         
         PAR14_HUMAN   1613 KQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1801
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhh...hhhhhh.......eeee.hhhhhhh...........eeeeeeeee...eee.............---.....eee.......eeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3se2 A 1532 KQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNP---TDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1720
                                  1541      1551      1561      1571      1581      1591      1601      1611      1621      1631      1641      1651      1661      1671      1681|   | 1691      1701      1711         
                                                                                                                                                                               1682   |                                  
                                                                                                                                                                                   1686

Chain B from PDB  Type:PROTEIN  Length:187
 aligned with PAR14_HUMAN | Q460N5 from UniProtKB/Swiss-Prot  Length:1801

    Alignment length:189
                                  1622      1632      1642      1652      1662      1672      1682      1692      1702      1712      1722      1732      1742      1752      1762      1772      1782      1792         
         PAR14_HUMAN   1613 KQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1801
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhhhhh.......eeeeeeeehhhhhhhhhhhh.hhhhh.--.......eeee.hhhhhh............eeeeeeeee...eee.....................eee.......eeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3se2 B 1532 KQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAG--AVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1720
                                  1541      1551      1561      1571      1581      1591      1601      1611      1621|  |  1631      1641      1651      1661      1671      1681      1691      1701      1711         
                                                                                                                   1622  |                                                                                               
                                                                                                                      1625

Chain C from PDB  Type:PROTEIN  Length:189
 aligned with PAR14_HUMAN | Q460N5 from UniProtKB/Swiss-Prot  Length:1801

    Alignment length:189
                                  1622      1632      1642      1652      1662      1672      1682      1692      1702      1712      1722      1732      1742      1752      1762      1772      1782      1792         
         PAR14_HUMAN   1613 KQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1801
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhhhhhhhh........eee..eeeeeee.hhhhhhh..........eeeeeeeeee...eee.........eee..eeeee..eee.......eeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3se2 C 1532 KQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1720
                                  1541      1551      1561      1571      1581      1591      1601      1611      1621      1631      1641      1651      1661      1671      1681      1691      1701      1711

Chain D from PDB  Type:PROTEIN  Length:189
 aligned with PAR14_HUMAN | Q460N5 from UniProtKB/Swiss-Prot  Length:1801

    Alignment length:189
                                  1622      1632      1642      1652      1662      1672      1682      1692      1702      1712      1722      1732      1742      1752      1762      1772      1782      1792         
         PAR14_HUMAN   1613 KQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1801
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----PARP-3se2D01 D:1537-1720                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) -----PARP-3se2D02 D:1537-1720                                                                                                                                                                 Pfam domains (2)
           Pfam domains (3) -----PARP-3se2D03 D:1537-1720                                                                                                                                                                 Pfam domains (3)
           Pfam domains (4) -----PARP-3se2D04 D:1537-1720                                                                                                                                                                 Pfam domains (4)
         Sec.struct. author ....eeeee....hhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhh........eee..eeeeeee.hhhhhhh...........eeeeeeeee...eee.....................eee.......eeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3se2 D 1532 KQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1720
                                  1541      1551      1561      1571      1581      1591      1601      1611      1621      1631      1641      1651      1661      1671      1681      1691      1701      1711

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 3SE2)

(no "CATH Domain" information available for 3SE2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ADP-ribosyl (56)

Family: PARP (21)

Homo sapiens (Human) (18)

1a	PARP-3se2D01	D:1537-1720
1b	PARP-3se2D02	D:1537-1720
1c	PARP-3se2D03	D:1537-1720
1d	PARP-3se2D04	D:1537-1720

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PAR14_HUMAN | Q460N5)

molecular function
	GO:0003950	NAD+ ADP-ribosyltransferase activity	Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

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	3se2
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3goy	SAME PROTEIN IN COMPLEX WITH 3AB AND IN A DIFFERENT SPACE- GROUP
3smi

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (13, 13)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (8, 8)

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Related Entries Specified in the PDB File