3KFP - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   HIV PROTEASE (PR) WITH INHIBITOR TL-3 BOUND, AND DMSOS IN EXO SITE

Authors :   C. D. Stout

Date :   27 Oct 09 (Deposition) - 23 Feb 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.77

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

Keywords :   Hiv-1, Protease, Exo Site, Aspartyl Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. L. Perryman, Q. Zhang, H. H. Soutter, R. Rosenfeld, D. E. Mcree, A. J. Olson, J. E. Elder, C. David Stout
Fragment-Based Screen Against Hiv Protease.
Chem. Biol. Drug Des. V. 75 257 2010
PubMed-ID: 20659109 | Reference-DOI: 10.1111/J.1747-0285.2009.00943.X

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	:	BL21.DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	POL
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Strain	:	R8

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

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	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE

Biological Unit 1 (3, 10)

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
2	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
3	DMS	6	Ligand/Ion	DIMETHYL SULFOXIDE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ILE A:47 , GLY A:48 , GLY A:49 , ILE A:50 , PRO A:81 , VAL A:82 , ILE A:84 , HOH A:306	BINDING SITE FOR RESIDUE 3TL A 200
2	AC2	SOFTWARE	THR A:12 , LYS A:14 , GLU A:65 , ILE A:66 , CYS A:67 , GLY A:68	BINDING SITE FOR RESIDUE DMS A 300
3	AC3	SOFTWARE	PRO A:39 , ILE A:62 , LEU A:63 , DMS A:302 , HOH A:305	BINDING SITE FOR RESIDUE DMS A 301
4	AC4	SOFTWARE	LYS A:14 , ILE A:15 , GLY A:16 , GLY A:17 , LEU A:63 , DMS A:301 , HOH A:305	BINDING SITE FOR RESIDUE DMS A 302
5	AC5	SOFTWARE	VAL A:11 , THR A:12 , CYS A:67	BINDING SITE FOR RESIDUE BME A 303

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

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

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

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_HV1Z2	509-578	1	A:20-89
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	POL_HV1Z2	511-522	1	A:22-33

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_HV1Z2	509-578	2	A:20-89
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	POL_HV1Z2	511-522	2	A:22-33

(no "Exon" information available for 3KFP)

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:99
 aligned with POL_HV1Z2 | P12499 from UniProtKB/Swiss-Prot  Length:1436

    Alignment length:99
                                   499       509       519       529       539       549       559       569       579         
            POL_HV1Z2   490 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 588
               SCOP domains d3kfpa_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 3kfpA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains ---RVP-3kfpA01 A:4-98                                                                             - Pfam domains
         Sec.struct. author .........eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------ASP_PROT_RETROV  PDB: A:20-89 UniProt: 509-578                        ---------- PROSITE (1)
                PROSITE (2) ---------------------ASP_PROTEASE------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3kfp A   1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF  99
                                    10        20        30        40        50        60        70        80        90

Chain A from PDB  Type:PROTEIN  Length:99
 aligned with Q903N5_9HIV1 | Q903N5 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
         Q903N5_9HIV1     1 PQITLWRRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF  99
               SCOP domains d3kfpa_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 3kfpA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains ---RVP-3kfpA01 A:4-98                                                                             - Pfam domains
         Sec.struct. author .........eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3kfp A   1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF  99
                                    10        20        30        40        50        60        70        80        90

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Retroviral protease (retropepsin) (591)

Protein domain: Human immunodeficiency virus type 1 protease (514)

Human immunodeficiency virus type 1 [TaxId: 11676] (424)

d3kfpa_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

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

Homologous Superfamily: Acid Proteases (745)

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: r8. (10)

3kfpA00

A:1-99

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_AA (368)

Family: RVP (212)

Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34) (HIV-1) (10)

RVP-3kfpA01

A:4-98

Asymmetric Unit(hide GO term definitions)

Chain A (POL_HV1Z2 | P12499)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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: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: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:0039526	modulation by virus of host apoptotic process	Any process in which a virus modulates the frequency, rate or extent of apoptosis of infected host cells.
	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:0039657	suppression by virus of host gene expression	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
	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:0075732	viral penetration into host nucleus	The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
	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: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:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	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.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0072494	host multivesicular body	A late endosome in which regions of the limiting host cell endosomal membrane invaginate to form internal vesicles; host membrane proteins that enter the internal vesicles are sequestered from the host cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0019013	viral nucleocapsid	The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Chain A (Q903N5_9HIV1 | Q903N5)

molecular function
	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: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: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.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kfp)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3kfp
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	POL_HV1Z2 \| P12499
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	Q903N5_9HIV1 \| Q903N5
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	3.4.23.16
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UniProtKB/Swiss-Prot
	POL_HV1Z2 \| P12499	:	1e28 1hxw 1p7q 1pro 1q94 1vij 1vik 2wkz 2wl0 2xye 2xyf 3kf0 3kfn 3kfr 3kfs 3w39 4dqb 4dqc 4dqe 4dqf 4dqg 4dqh 4e43 4ej8 4ejd 4ejk 4ejl 4k4p 4k4q 4k4r
	Q903N5_9HIV1 \| Q903N5	:	3kf0 3kfn 3kfr 3kfs 4e43
UniProtKB/TrEMBL
	Q903N5_9HIV1 \| Q903N5	:	2hb4 2pc0

2az8	HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, WILD TYPE
3kf0	HIV PROTEASE WITH FRAGMENT 4D9 BOUND
3kf1	HIV PROTEASE (PR) DIMER WITHOUT INHIBITOR; ACETATE IN EXO SITE
3kfn	HIV PROTEASE (PR) WITH INHIBITOR TL-3 AND FRAGMENT HIT 4D9 BY SOAKING
3kfr	HIV PROTEASE (PR) DIMER WITH INHIBITOR TL-3 BOUND AND FRAGMENT 1F1 IN THE OUTSIDE/TOP OF FLAP
3kfs	HIV PROTEASE (PR) DIMER WITH INHIBITOR TL-3 BOUND AND FRAGMENT 2F4 IN THE OUTSIDE/TOP OF FLAP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (45, 49)

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Related Entries

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Related Entries Specified in the PDB File