2HAH - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE STRUCTURE OF FIV 12S PROTEASE IN COMPLEX WITH TL-3

Authors :   H. Heaslet, Y. C. Lin, J. H. Elder, C. D. Stout

Date :   12 Jun 06 (Deposition) - 13 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Retroviral, Protease, Aspartyl, Feline, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Heaslet, Y. C. Lin, K. Tam, B. E. Torbett, J. H. Elder, C. D. Stout
Crystal Structure Of An Fiv/Hiv Chimeric Protease Complexed With The Broad-Based Inhibitor, Tl-3.
Retrovirology V. 4 1 2007
PubMed-ID: 17212810 | Reference-DOI: 10.1186/1742-4690-4-1

Molecule 1 - PROTEASE
	Chains	:	A
	EC Number	:	3.4.23.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A(+)
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 39-154
	Gene	:	POL
	Mutation	:	YES
	Organism Scientific	:	FELINE IMMUNODEFICIENCY VIRUS (ISOLATE PETALUMA)
	Organism Taxid	:	11674
	Strain	:	ISOLATE PETALUMA
	Synonym	:	RETROPEPSIN

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

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

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	3TL	2	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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:13 , PRO A:24 , ILE A:25 , ASP A:30 , GLY A:32 , ALA A:33 , ASP A:34 , GLN A:54 , MET A:55 , ILE A:56 , GLY A:57 , GLY A:58 , ILE A:59 , PRO A:98 , VAL A:99 , HOH A:231	BINDING SITE FOR RESIDUE 3TL A 201

(no "SS Bond" information available for 2HAH)

(no "Cis Peptide Bond" information available for 2HAH)

(no "SAP(SNP)/Variant" information available for 2HAH)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_PROT_RETROV	PS50175	Aspartyl protease, retroviral-type family profile.	POL_FIVPE	63-144	1	A:25-106
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	POL_FIVPE	65-76	1	A:27-38

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_PROT_RETROV	PS50175	Aspartyl protease, retroviral-type family profile.	POL_FIVPE	63-144	2	A:25-106
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	POL_FIVPE	65-76	2	A:27-38

(no "Exon" information available for 2HAH)

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:112
 aligned with POL_FIVPE | P16088 from UniProtKB/Swiss-Prot  Length:1124

    Alignment length:113
                                                                                  97                                                         
                                                                                96 |                                                         
                                    52        62        72        82        92   | | 101       111       121       131       141       151   
            POL_FIVPE    43 GTTTTLEKRPEILIFVNGYPIKFLLDTGADITILNRRDFQVKNSIENGRQNMIG-VGGGKRGTNYINVHLEIRDENYKTQCIFGNVCVLEDNSLIQPLLGRDNMIKFNIRLVM 154
               SCOP domains d2haha_ A: automated matches                                                                                      SCOP domains
               CATH domains 2hahA00 A:5-116 Acid Proteases                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeee.......eee.hhh.....eeeeee-eeee..eeeeeeeeeeeeeee.......eeeeeeeeee.......eeehhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------ASP_PROT_RETROV  PDB: A:25-106 UniProt: 63-144                                     ---------- PROSITE (1)
                PROSITE (2) ----------------------ASP_PROTEASE------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2hah A   5 GTTTTLEKRPEILIFVNGYPIKFLLDTGADITVLNRRDFQVKNSIENGRQ-MIGGIGGFIRGTNYINVHLEIRDENYKTQCIFGNVCVLEDNSTPVNILGRDNMIKFNIRLVM 116
                                    14        24        34        44        54 |      63        73        83        93       103       113   
                                                                            54 |                                                             
                                                                              55

Chain A from PDB  Type:PROTEIN  Length:112
 aligned with Q66972_9RETR | Q66972 from UniProtKB/TrEMBL  Length:1124

    Alignment length:113
                                                                                  97                                                         
                                                                                96 |                                                         
                                    52        62        72        82        92   | | 101       111       121       131       141       151   
         Q66972_9RETR    43 GTTTTLEKRPEILIFVNGYPIKFLLDTGADITILNRRDFQVKNSIENGRQNMIG-VGGGKRGTNYINVHLEIRDENYKTQCIFGNVCVLEDNSLIQPLLGRDNMIKFNIRLVM 154
               SCOP domains d2haha_ A: automated matches                                                                                      SCOP domains
               CATH domains 2hahA00 A:5-116 Acid Proteases                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeee.......eee.hhh.....eeeeee-eeee..eeeeeeeeeeeeeee.......eeeeeeeeee.......eeehhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2hah A   5 GTTTTLEKRPEILIFVNGYPIKFLLDTGADITVLNRRDFQVKNSIENGRQ-MIGGIGGFIRGTNYINVHLEIRDENYKTQCIFGNVCVLEDNSTPVNILGRDNMIKFNIRLVM 116
                                    14        24        34        44        54 |      63        73        83        93       103       113   
                                                                            54 |                                                             
                                                                              55

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Retroviral protease (retropepsin) (591)

Protein domain: automated matches (39)

Feline immunodeficiency virus (isolate petaluma) [TaxId: 11674] (1)

d2haha_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Cathepsin D, subunit A; domain 1 (745)

Homologous Superfamily: Acid Proteases (745)

Feline immunodeficiency virus (isolate petaluma). Organism_taxid: 11674. Strain: isolate petaluma. (1)

2hahA00

A:5-116

(no "Pfam Domain" information available for 2HAH)

Asymmetric Unit(hide GO term definitions)

Chain A (Q66972_9RETR | Q66972)

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: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:0046080	dUTP metabolic process	The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
	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.

Chain A (POL_FIVPE | P16088)

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:0004170	dUTP diphosphatase activity	Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004533	exoribonuclease H activity	Catalysis of the exonucleolytic cleavage of RNA to 5'-phosphomonoester oligonucleotides in both 5' to 3' and 3' to 5' directions.
	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: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:0090503	RNA phosphodiester bond hydrolysis, exonucleolytic	The chemical reactions and pathways involving the hydrolysis of terminal 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:0046080	dUTP metabolic process	The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
	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:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	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.

Asymmetric Unit
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Access by PDB/NDB ID
	2hah
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	Q66972_9RETR \| Q66972
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	3.4.23.16
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UniProtKB/Swiss-Prot
	POL_FIVPE \| P16088	:	1b11 1dut 1f7d 1f7k 1f7n 1f7o 1f7p 1f7q 1f7r 1fiv 2fiv 3fiv 3ogp 3ogq 4fiv 4mq3 4pa1 5fiv 6fiv
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	Q66972_9RETR \| Q66972	:	4fiv

2az8	STRUCTURE OF WILD-TYPE HIV PROTEASE IN COMPLEX WITH TL-3
5fiv	STRUCTURE OF WILD-TYPE FIV PROTEASE IN COMPLEX WITH TL-3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (28, 52)

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Related Entries Specified in the PDB File