3NF6 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURAL BASIS FOR A NEW MECHANISM OF INHIBITION OF HIV INTEGRASE IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DESIGN

Authors :   T. S. Peat, J. Newman, J. J. Deadman, D. Rhodes

Date :   09 Jun 10 (Deposition) - 27 Apr 11 (Release) - 02 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Integrase, Integration, Dna, See Mutations, Intra-Cellular, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. I. Rhodes, T. S. Peat, N. Vandegraaff, D. Jeevarajah, G. Le, E. D. Jones, J. A. Smith, J. A. Coates, L. J. Winfield, N. Thienthong, J. Newman, D. Lucent, J. H. Ryan, G. P. Savage, C. L. Francis, J. J. Deadman
Structural Basis For A New Mechanism Of Inhibition Of Hiv-1 Integrase Identified By Fragment Screening And Structure-Based Design
Antivir. Chem. Chemother. V. 21 155 2011
PubMed-ID: 21602613 | Reference-DOI: 10.3851/IMP1716

Molecule 1 - INTEGRASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 50-212
	Mutation	:	YES
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 16)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	CL	2	Ligand/Ion	CHLORIDE ION
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
4	IMV	4	Ligand/Ion	5-[(2-OXO-2,3-DIHYDRO-1H-INDOL-1-YL)METHYL]-1,3-BENZODIOXOLE-4-CARBOXYLIC ACID
5	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:66 , HIS A:67 , LYS A:111 , LYS A:136 , LYS A:159 , HOH A:256	BINDING SITE FOR RESIDUE SO4 A 2
02	AC2	SOFTWARE	HOH A:13 , LYS A:71 , ARG A:166 , HIS A:171 , LEU A:172	BINDING SITE FOR RESIDUE SO4 A 4
03	AC3	SOFTWARE	ASN A:184 , HIS A:185 , HOH A:244 , GLY B:106 , PRO B:109	BINDING SITE FOR RESIDUE EDO A 213
04	AC4	SOFTWARE	SER A:123 , THR A:125 , HOH A:239	BINDING SITE FOR RESIDUE CL A 1
05	AC5	SOFTWARE	GLU A:85 , GLU A:87 , PHE A:100 , LYS A:103 , LEU A:104 , ARG A:107 , HOH A:259 , ARG B:107	BINDING SITE FOR RESIDUE ACY A 214
06	AC6	SOFTWARE	ALA A:169 , GLU A:170 , HIS A:171 , THR A:174 , GLN B:95 , TYR B:99 , LEU B:102 , THR B:125 , ALA B:128 , ALA B:129 , TRP B:132	BINDING SITE FOR RESIDUE IMV A 215
07	AC7	SOFTWARE	VAL A:79 , GLY A:82 , ILE A:84 , VAL A:150 , MET A:154 , GLU A:157 , HIS A:183	BINDING SITE FOR RESIDUE IMV A 230
08	AC8	SOFTWARE	THR B:66 , HIS B:67 , LYS B:111 , LYS B:136 , LYS B:159 , HOH B:255	BINDING SITE FOR RESIDUE SO4 B 1
09	AC9	SOFTWARE	HOH B:14 , LYS B:71 , HIS B:171 , LEU B:172 , HOH B:259	BINDING SITE FOR RESIDUE SO4 B 3
10	BC1	SOFTWARE	GLY A:106 , ARG A:107 , EDO B:4 , TYR B:83 , ASN B:184 , HIS B:185 , GLY B:197	BINDING SITE FOR RESIDUE EDO B 213
11	BC2	SOFTWARE	ARG A:187 , HOH B:29 , GLU B:92 , THR B:93 , GLY B:94 , HOH B:254	BINDING SITE FOR RESIDUE EDO B 214
12	BC3	SOFTWARE	ARG A:107 , PRO A:109 , GLY B:197 , VAL B:201 , EDO B:213	BINDING SITE FOR RESIDUE EDO B 4
13	BC4	SOFTWARE	SER B:123 , THR B:125 , HOH B:227	BINDING SITE FOR RESIDUE CL B 2
14	BC5	SOFTWARE	ARG A:107 , HOH A:259 , GLU B:85 , GLU B:87 , PHE B:100 , LYS B:103 , LEU B:104 , ARG B:107	BINDING SITE FOR RESIDUE ACY B 215
15	BC6	SOFTWARE	GLN A:95 , TYR A:99 , LEU A:102 , THR A:125 , ALA A:128 , ALA A:129 , TRP A:132 , HOH A:246 , ALA B:169 , GLU B:170 , HIS B:171 , THR B:174 , MET B:178 , HOH B:248	BINDING SITE FOR RESIDUE IMV B 216
16	BC7	SOFTWARE	VAL B:79 , GLY B:82 , ILE B:84 , VAL B:150 , ILE B:151 , MET B:154 , GLU B:157 , HIS B:183	BINDING SITE FOR RESIDUE IMV B 231

(no "SS Bond" information available for 3NF6)

(no "Cis Peptide Bond" information available for 3NF6)

(no "SAP(SNP)/Variant" information available for 3NF6)

(no "PROSITE Motif" information available for 3NF6)

(no "Exon" information available for 3NF6)

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
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Chain A from PDB  Type:PROTEIN  Length:149
 aligned with POL_HV1N5 | P12497 from UniProtKB/Swiss-Prot  Length:1435

    Alignment length:153
                                  1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353   
           POL_HV1N5   1204 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQ 1356
               SCOP domains d3nf6a_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nf6 A   57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRK----GYSAGERIVDIIATDIQ  209
                                    66        76        86        96       106       116       126       136       146       156       166       176       186 |    |196       206   
                                                                                                                                                             188  193

Chain A from PDB  Type:PROTEIN  Length:149
 aligned with Q76353_9HIV1 | Q76353 from UniProtKB/TrEMBL  Length:288

    Alignment length:153
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
        Q76353_9HIV1     57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQ  209
               SCOP domains d3nf6a_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nf6 A   57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRK----GYSAGERIVDIIATDIQ  209
                                    66        76        86        96       106       116       126       136       146       156       166       176       186 |    |196       206   
                                                                                                                                                             188  193

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with POL_HV1N5 | P12497 from UniProtKB/Swiss-Prot  Length:1435

    Alignment length:153
                                  1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353   
           POL_HV1N5   1204 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQ 1356
               SCOP domains d3nf6b_ B: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) rve-3nf6B01 B:57-162                                                                                      ----------------------------------------------- Pfam domains (1)
           Pfam domains (2) rve-3nf6B02 B:57-162                                                                                      ----------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nf6 B   57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRK----GYSAGERIVDIIATDIQ  209
                                    66        76        86        96       106       116       126       136       146       156       166       176       186 |    |196       206   
                                                                                                                                                             188  193

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with Q76353_9HIV1 | Q76353 from UniProtKB/TrEMBL  Length:288

    Alignment length:153
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
        Q76353_9HIV1     57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQ  209
               SCOP domains d3nf6b_ B: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) rve-3nf6B01 B:57-162                                                                                      ----------------------------------------------- Pfam domains (1)
           Pfam domains (2) rve-3nf6B02 B:57-162                                                                                      ----------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nf6 B   57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRK----GYSAGERIVDIIATDIQ  209
                                    66        76        86        96       106       116       126       136       146       156       166       176       186 |    |196       206   
                                                                                                                                                             188  193

Legend:		→ Mismatch	(orange background)
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	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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: Retroviral integrase, catalytic domain (152)

Protein domain: automated matches (90)

Human immunodeficiency virus 1 [TaxId: 11676] (61)

1a	d3nf6a_	A:
1b	d3nf6b_	B:

(no "CATH Domain" information available for 3NF6)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RNase_H (288)

Family: rve (46)

Human immunodeficiency virus 1 (6)

1a	rve-3nf6B01	B:57-162
1b	rve-3nf6B02	B:57-162

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (POL_HV1N5 | P12497)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0005546	phosphatidylinositol-4,5-bisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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,B (Q76353_9HIV1 | Q76353)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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: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:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nf6)

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	3nf6
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		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
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	POL_HV1N5 \| P12497
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q76353_9HIV1 \| Q76353
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
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	POL_HV1N5 \| P12497
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q76353_9HIV1 \| Q76353
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1bhl	CACODYLATED CATALYTIC DOMAIN OF HIV-1 INTEGRASE
1bi4	CATALYTIC DOMAIN OF HIV-1 INTEGRASE
1biu	HIV-1 INTEGRASE CORE DOMAIN COMPLEXED WITH MG++
1ex4	HIV-1 INTEGRASE CATALYTIC CORE AND C-TERMINAL DOMAIN
1k6y	TWO-DOMAIN FRAGMENT OF HIV-1 INTEGRASE
3nf7	HIV-1 INTEGRASE, DIFFERENT INHIBITOR
3nf8	HIV-1 INTEGRASE, DIFFERENT INHIBITOR
3nf9	HIV-1 INTEGRASE, DIFFERENT INHIBITOR
3nfa	HIV-1 INTEGRASE, DIFFERENT INHIBITOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 16)

Sites (16, 16)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (48, 62)

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Still Images

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Databases

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File