4IOX - JenaLib

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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)

Title :   THE STRUCTURE OF THE HERPES SIMPLEX VIRUS DNA-PACKAGING MOTOR PUL15 C-TERMINAL NUCLEASE DOMAIN PROVIDES INSIGHTS INTO CLEAVAGE OF CONCATEMERIC VIRAL GENOME PRECURSORS

Authors :   S. Selvarajan Sigamani, H. Zhao, Y. Kamau, L. Tang

Date :   08 Jan 13 (Deposition) - 01 May 13 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.46

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)

Keywords :   Nuclease, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Selvarajan Sigamani, H. Zhao, Y. N. Kamau, J. D. Baines, L. Tang
The Structure Of The Herpes Simplex Virus Dna-Packaging Terminase Pul15 Nuclease Domain Suggests An Evolutionary Lineage Among Eukaryotic And Prokaryotic Viruses.
J. Virol. V. 87 7140 2013
PubMed-ID: 23596306 | Reference-DOI: 10.1128/JVI.00311-13

Molecule 1 - TRIPARTITE TERMINASE SUBUNIT UL15
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN (UNP RESIDUES 471-735)
	Gene	:	UL15
	Organism Common	:	HHV-1
	Organism Scientific	:	HUMAN HERPESVIRUS 1
	Organism Taxid	:	10298
	Synonym	:	DNA-PACKAGING PROTEIN UL15, TERMINASE LARGE SUBUNIT

Molecule 2 - PEPTIDE
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEE REMARK 999
	Organism Common	:	HHV-1
	Organism Scientific	:	HUMAN HERPESVIRUS 1
	Organism Taxid	:	10298

		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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
5	UNK	6	Mod. Amino Acid

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
5	UNK	-1	Mod. Amino Acid

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL
4	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL
5	UNK	-1	Mod. Amino Acid

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL
4	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL
5	UNK	-1	Mod. Amino Acid

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL
4	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL
5	UNK	-1	Mod. Amino Acid

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:491 , LEU A:499 , TYR A:529 , ARG A:530 , HOH A:914 , LEU C:499 , TYR C:529 , ARG C:530	BINDING SITE FOR RESIDUE PGE A 801
2	AC2	SOFTWARE	HIS A:595 , GLU A:599	BINDING SITE FOR RESIDUE PEG A 802
3	AC3	SOFTWARE	ARG A:577 , HIS A:597 , LEU A:618 , PHE A:619 , TYR A:620 , HIS A:621 , GLU C:623	BINDING SITE FOR RESIDUE PG4 A 803
4	AC4	SOFTWARE	GLY A:626 , THR C:598 , HIS C:601	BINDING SITE FOR RESIDUE ACT A 804

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

Asymmetric Unit

No.	Residues
1	Arg B:602	-	Leu B:603
2	Gln C:721	-	Ala C:722

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

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

(no "Exon" information available for 4IOX)

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:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh......hhhhh..eeeeeee..........eeeeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhh....hhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iox A 476 PVLTKSAGERFLLYRPSTTTNSGLMAPDLYVYVDPAFTANTRASGTGVAVVGRYRDDYIIFALEHFFLRALTGSAPADIARCVVHSLTQVLALHPGAFRGVRVAVEGNSSQDSAVAIATHVHTEMHRGPELLFYHCEPPGSAVLYPFFLLNKQKTPAFEHFIKKFNSGGVMASQEIVSATVRLQTDPVEYLLEQLNNLTSDDLMVAVIMAIYLAAQAGPPHTFAP 730
                                   485       495       505       515       525       535       545       555       565       575       585       595      |616       626       636       646       656       666       676       705       715       725     
                                                                                                                                                        602|                                                                    685|                         
                                                                                                                                                         614                                                                     705

Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh......hhh.eeeeeeeeee...eeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhh......eeee...................hhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhh....hhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4iox B 477 VLTKSAGERFLLYRPSTTTNSGLMAPDLYVYVDPAGTGVAVVGRYRDDYIIFALEHFFLGSAPADIARCVVHSLTQVLALHPGAFRGVRVAVEGNSSQDSAVAIATHVHTEMHRLLSGPELLFYHCEPPGSAVLYPFFLLNKQKTPAFEHFIKKFNSGGVMASQEIVSATVRLQTDPVEYLLEQLNNLTSDDLMVAVIMAIYLAAQAGPPHTFAPI 731
                                   486       496       506    || 524       534       548       558       568       578       588       598     ||616       626       636       646       656       666       676       705       715       725      
                                                            511|                    543|                                                     604|                                                                     685|                          
                                                             520                     548                                                      613                                                                      705

Chain C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh......hhhhh..eeeeeee...eeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhh.......hhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iox C 476 PVLTKSAGERFLLYRPSTTTNSGLMAPDLYVYVDPAGTGVAVVGRYRDDYIIFALEHFFLGSAPADIARCVVHSLTQVLALHPGAFRGVRVAVEGNSSQDSAVAIATHVHTEMHRLLGPELLFYHCEPPGSAVLYPFFLLNKQKTPAFEHFIKKFNSGGVMASQEIVSATVRLQTDPVEYLLEQLNNLTETVSDDLMVAVIMAIYLAAQAGPPHTFAPIT 732
                                   485       495       505     ||523       533       543|      557       567       577       587       597      |616       626       636       646       656       666       676       686 ||    712       722       732
                                                             511|                    543|                                                     604|                                                                       688|                           
                                                              520                     548                                                      614                                                                        705

Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4iox D 800 xxxxxx 805
                            ||||||
                          800-UNK|
                           801-UNK
                            802-UNK
                             803-UNK
                              804-UNK
                               805-UNK

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 4IOX)

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

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

Asymmetric Unit(hide GO term definitions)

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	Ligands, Modified Residues, Ions
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PG4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PGE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UNK	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg B:602 - Leu B:603	[ RasMol ]
		Gln C:721 - Ala C:722	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

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

Description

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Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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