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Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE CRYSTAL STRUCTURE OF XMRV PROTEASE COMPLEXED WITH TL-3

Authors :   M. Li, A. Gustchina, A. Wlodawer

Date :   27 Jun 11 (Deposition) - 12 Oct 11 (Release) - 04 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Beta Sheet And Dimer, Protease, Peptide Inhibitor, Tl-3 Pepstatina, Virus, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Li, A. Gustchina, K. Matuz, J. Tozser, S. Namwong, N. E. Goldfarb, B. M. Dunn, A. Wlodawer
Structural And Biochemical Characterization Of The Inhibito Complexes Of Xenotropic Murine Leukemia Virus-Related Virus Protease.
Febs J. V. 278 4413 2011
PubMed-ID: 21951660 | Reference-DOI: 10.1111/J.1742-4658.2011.08364.X

Molecule 1 - GAG-PRO-POL POLYPROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST-521
	Expression System Strain	:	BL21(DE3)TONA PRARE
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 533-657
	Gene	:	GAG-POL
	Organism Scientific	:	DG-75 MURINE LEUKEMIA VIRUS
	Organism Taxid	:	114654

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	3TL	1	Ligand/Ion	BENZYL [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-DIBENZYL-8,9-DIHYDROXY-1,16-DIMETHYL-4,13-BIS(1-METHYLETHYL)-2,5,12,15,18-PENTAOXO-20-PHENYL-19-OXA-3,6,11,14,17-PENTAAZAICOS-1-YL]CARBAMATE
2	FMT	6	Ligand/Ion	FORMIC ACID
3	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:32 , GLY A:34 , GLN A:36 , HIS A:37 , PRO A:46 , ALA A:52 , TRP A:53 , VAL A:54 , GLN A:55 , GLY A:56 , ALA A:57 , TRP A:65 , THR A:67 , PRO A:89 , TYR A:90 , LEU A:92 , HOH A:130 , HOH A:163 , HOH A:185 , ASP B:32 , GLY B:34 , ALA B:35 , GLN B:36 , HIS B:37 , TRP B:53 , VAL B:54 , GLN B:55 , GLY B:56 , ALA B:57 , TRP B:65 , PRO B:89 , TYR B:90 , LEU B:92 , FMT B:129	BINDING SITE FOR RESIDUE 3TL A 126
2	AC2	SOFTWARE	HIS A:37 , HIS A:80 , SER A:81 , HOH A:183 , HOH A:261	BINDING SITE FOR RESIDUE FMT A 127
3	AC3	SOFTWARE	SER A:48 , THR A:66 , THR A:67 , ASP A:68 , SER A:81 , HOH A:148 , HOH A:195 , HOH A:251	BINDING SITE FOR RESIDUE FMT A 128
4	AC4	SOFTWARE	GLY A:45 , HOH A:189 , HIS B:37 , HIS B:80 , SER B:81	BINDING SITE FOR RESIDUE FMT B 126
5	AC5	SOFTWARE	GLY B:111 , NA B:130 , HOH B:157 , HOH B:220	BINDING SITE FOR RESIDUE FMT B 127
6	AC6	SOFTWARE	LEU B:40 , THR B:41 , GLN B:42 , PRO B:91 , HOH B:142 , HOH B:227	BINDING SITE FOR RESIDUE FMT B 128
7	AC7	SOFTWARE	3TL A:126 , TRP B:53 , HOH B:185 , HOH B:215	BINDING SITE FOR RESIDUE FMT B 129
8	AC8	SOFTWARE	PHE B:107 , GLY B:109 , GLY B:111 , FMT B:127 , HOH B:157 , HOH B:179	BINDING SITE FOR RESIDUE NA B 130

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:15	-	Pro A:16
2	Glu B:15	-	Pro B:16

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

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

(no "Exon" information available for 3SLZ)

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:114
 aligned with Q9E7M1_9GAMR | Q9E7M1 from UniProtKB/TrEMBL  Length:1733

    Alignment length:114
                                   552       562       572       582       592       602       612       622       632       642       652    
         Q9E7M1_9GAMR   543 EPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQV 656
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee..eeeeeee.......ee......eeeeeeeee....eeeeeee..eeeee..eeeee..ee.......eehhhhhhhhh.eeeee..eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3slz A  11 EPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQV 124
                                    20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q9E7M1_9GAMR | Q9E7M1 from UniProtKB/TrEMBL  Length:1733

    Alignment length:114
                                   552       562       572       582       592       602       612       622       632       642       652    
         Q9E7M1_9GAMR   543 EPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQV 656
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee..eeeeeee.......ee......eeeeeeeee....eeeeeee..eeee....eeee..ee.......eehhhhhhhhh.eee......eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3slz B  11 EPPPEPRITLKVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRKVHLATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQV 124
                                    20        30        40        50        60        70        80        90       100       110       120

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 3SLZ)

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

(no "Pfam Domain" information available for 3SLZ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q9E7M1_9GAMR | Q9E7M1)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	GO:0003964	RNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	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:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0015074	DNA integration	The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0006278	RNA-dependent DNA biosynthetic process	A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
	GO:0075713	establishment of integrated proviral latency	A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
	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:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019068	virion assembly	A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
cellular component
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:15 - Pro A:16	[ RasMol ]
		Glu B:15 - Pro B:16	[ RasMol ]

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	Q9E7M1_9GAMR \| Q9E7M1	:	3sm1 3sm2 4exh

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Gene Ontology (28, 28)

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