3N4Q - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HUMAN CYTOMEGALOVIRUS TERMINASE NUCLEASE DOMAIN, MN SOAKED

Authors :   M. Nadal, P. J. Mas, A. G. Blanco, C. Arnan, M. Sola, D. J. Hart, M. Coll

Date :   22 May 10 (Deposition) - 13 Oct 10 (Release) - 13 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Terminase, Nuclease, Human Cytomegalovirus, Hcmv, Herpesvirus, Dna Packaging, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nadal, P. J. Mas, A. G. Blanco, C. Arnan, M. Sola, D. J. Hart, M. Coll
Structure And Inhibition Of Herpesvirus Dna Packaging Terminase Nuclease Domain.
Proc. Natl. Acad. Sci. Usa V. 107 16078 2010
PubMed-ID: 20805464 | Reference-DOI: 10.1073/PNAS.1007144107

Molecule 1 - TERMINASE SUBUNIT UL89 PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 418-674
	Organism Scientific	:	HUMAN HERPESVIRUS 5
	Organism Taxid	:	10363
	Strain	:	TOWNE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	MN	8	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MN A:2 , HOH A:23 , ASP A:463 , ASP A:651	BINDING SITE FOR RESIDUE MN A 1
02	AC2	SOFTWARE	MN A:1 , HOH A:49 , ASP A:463 , PRO A:464 , GLU A:534	BINDING SITE FOR RESIDUE MN A 2
03	AC3	SOFTWARE	MN B:4 , HOH B:31 , ASP B:463 , ASP B:651	BINDING SITE FOR RESIDUE MN B 3
04	AC4	SOFTWARE	MN B:3 , HOH B:50 , HOH B:51 , ASP B:463 , GLU B:534	BINDING SITE FOR RESIDUE MN B 4
05	AC5	SOFTWARE	MN C:6 , HOH C:52 , HOH C:53 , ASP C:463 , GLU C:534	BINDING SITE FOR RESIDUE MN C 5
06	AC6	SOFTWARE	MN C:5 , HOH C:54 , HOH C:55 , ASP C:463 , ASP C:651	BINDING SITE FOR RESIDUE MN C 6
07	AC7	SOFTWARE	MN D:8 , HOH D:56 , ASP D:463 , ASP D:651	BINDING SITE FOR RESIDUE MN D 7
08	AC8	SOFTWARE	MN D:7 , HOH D:35 , ASP D:463 , GLU D:534	BINDING SITE FOR RESIDUE MN D 8
09	AC9	SOFTWARE	ASP A:439 , GLU A:618 , ASN B:447	BINDING SITE FOR RESIDUE MG A 675
10	BC1	SOFTWARE	ASN A:447 , ASP B:439 , GLU B:618 , ARG D:581	BINDING SITE FOR RESIDUE MG B 2
11	BC2	SOFTWARE	ASN C:447 , THR C:448 , ASP D:439 , GLU D:618	BINDING SITE FOR RESIDUE MG D 3
12	BC3	SOFTWARE	ASP C:439 , GLU C:618 , ASN D:447	BINDING SITE FOR RESIDUE MG C 4

(no "SS Bond" information available for 3N4Q)

(no "Cis Peptide Bond" information available for 3N4Q)

(no "SAP(SNP)/Variant" information available for 3N4Q)

(no "PROSITE Motif" information available for 3N4Q)

(no "Exon" information available for 3N4Q)

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:216
 aligned with TRM3_HCMVA | P16732 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:246
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668      
           TRM3_HCMVA   429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPAFTTNRKASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRVTLAEGTTARYSAKRQNRISDDLIIAVIMATYLCDDIHAIRFRVS 674
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhheee.............eeeeeee..--------.eeeeeeeee..eeeeeeeeee..---..hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhh....-------------------.hhhhhhhhhhhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n4q A 429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPA--------GTGVAAVGAYRHQFLIYGLEHFFL---SESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHR-------------------SDDLIIAVIMATYLCDDIHAIRFRVS 674
                                   438       448       458      |  -     | 478       488        |-  |    508       518       528       538       548       558       568       578       588       598       608       618       628|        -         -|      658       668      
                                                              465      474                    497 501                                                                                                                             629                 649

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with TRM3_HCMVA | P16732 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:246
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668      
           TRM3_HCMVA   429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPAFTTNRKASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRVTLAEGTTARYSAKRQNRISDDLIIAVIMATYLCDDIHAIRFRVS 674
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhheee.hhhh........eeeeeee..------...eeeeeeeee..eeeeeeeeee..----.hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhh..eeeee.ee.....ee.......hhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhh.....---------------....hhhhhhhhhhhhh........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n4q B 429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPA------ASGTGVAAVGAYRHQFLIYGLEHFFL----ESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRV---------------NRISDDLIIAVIMATYLCDDIHAIRFRVS 674
                                   438       448       458      |  -   |   478       488        |-   |   508       518       528       538       548       558       568       578       588       598       608       618       628 |       -       648       658       668      
                                                              465    472                      497  502                                                                                                                             630             646

Chain C from PDB  Type:PROTEIN  Length:219
 aligned with TRM3_HCMVA | P16732 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:245
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668     
           TRM3_HCMVA   429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPAFTTNRKASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRVTLAEGTTARYSAKRQNRISDDLIIAVIMATYLCDDIHAIRFRV 673
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhheee.............eeeeeee..------...eeeeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhh....eeeee.ee.....ee.......hhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhh..--------------------..hhhhhhhhhhhhhh...hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n4q C 429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPA------ASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNL--------------------ISDDLIIAVIMATYLCDDIHAIRFRV 673
                                   438       448       458      |  -   |   478       488       498       508       518       528       538       548       558       568       578       588       598       608       618        |-         -       648       658       668     
                                                              465    472                                                                                                                                                        627                  648

Chain D from PDB  Type:PROTEIN  Length:214
 aligned with TRM3_HCMVA | P16732 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:246
                                   438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668      
           TRM3_HCMVA   429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPAFTTNRKASGTGVAAVGAYRHQFLIYGLEHFFLRDLSESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHRVTLAEGTTARYSAKRQNRISDDLIIAVIMATYLCDDIHAIRFRVS 674
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) DNA_pack_C-3n4qD01 D:429-674                                                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) DNA_pack_C-3n4qD02 D:429-674                                                                                                                                                                                                                           Pfam domains (2)
           Pfam domains (3) DNA_pack_C-3n4qD03 D:429-674                                                                                                                                                                                                                           Pfam domains (3)
           Pfam domains (4) DNA_pack_C-3n4qD04 D:429-674                                                                                                                                                                                                                           Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhheee.............eeeeeee..-------...eeeeeeee..eeeeeeee...-----hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhh....eeeee.ee.....ee......hhhhhhhhhhhhhhhh..eeee............hhhhhhhhhhhh...--------------------..hhhhhhhhhhhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n4q D 429 LITDQSREEFDILRYSTLNTNAYDYFGKTLYVYLDPA-------SGTGVAAVGAYRHQFLIYGLEHFF-----ESSEVAIAECAAHMIISVLSLHPYLDELRIAVEGNTNQAAAVRIACLIRQSVQSSTLIRVLFYHTPDQNHIEQPFYLMGRDKALAVEQFISRFNSGYIKASQELVSYTIKLSHDPIEYLLEQIQNLHR--------------------DDLIIAVIMATYLCDDIHAIRFRVS 674
                                   438       448       458      |  -    |  478       488       | -   |   508       518       528       538       548       558       568       578       588       598       608       618       628|        -         - |     658       668      
                                                              465     473                    496   502                                                                                                                            629                  650

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 3N4Q)

(no "CATH Domain" information available for 3N4Q)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: DNA_pack_C (3)

Human cytomegalovirus (strain AD169) (HHV-5) (Human herpesvirus 5) (2)

1a	DNA_pack_C-3n4qD01	D:429-674
1b	DNA_pack_C-3n4qD02	D:429-674
1c	DNA_pack_C-3n4qD03	D:429-674
1d	DNA_pack_C-3n4qD04	D:429-674

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TRM3_HCMVA | P16732)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
biological process
	GO:0006323	DNA packaging	Any process in which DNA and associated proteins are formed into a compact, orderly structure.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3n4q)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3n4q
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	TRM3_HCMVA \| P16732
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	TRM3_HCMVA \| P16732
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	TRM3_HCMVA \| P16732	:	3n4p

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Pfam Domains (1, 4)

Gene Ontology (5, 5)

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