3VQ5 - JenaLib

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:65 , HIS A:67 , GLU A:92 , CD A:1002 , ASP B:131	BINDING SITE FOR RESIDUE CD A 1001
02	AC2	SOFTWARE	CYS A:65 , GLU A:92 , ASP A:116 , CD A:1001 , CL A:1003 , HOH A:1103 , HOH A:1106	BINDING SITE FOR RESIDUE CD A 1002
03	AC3	SOFTWARE	CYS A:65 , ASP A:116 , ASN A:120 , CD A:1002	BINDING SITE FOR RESIDUE CL A 1003
04	AC4	SOFTWARE	LYS A:71 , HIS A:171 , LEU A:172 , HOH A:1148	BINDING SITE FOR RESIDUE SO4 A 1004
05	AC5	SOFTWARE	THR A:66 , HIS A:67 , LYS A:159 , ARG B:127 , HOH B:438	BINDING SITE FOR RESIDUE SO4 A 1005
06	AC6	SOFTWARE	GLN A:95 , GLY A:123 , ALA A:124 , THR A:125 , ARG A:187 , HOH A:1108	BINDING SITE FOR RESIDUE SO4 A 1006
07	AC7	SOFTWARE	ARG A:107 , PRO A:109 , ILE A:204 , ASP A:207 , HIS B:185 , GLY B:197 , GLU B:198	BINDING SITE FOR RESIDUE MMJ A 1007
08	AC8	SOFTWARE	ASP A:131 , CYS B:65 , HIS B:67 , GLU B:92 , CD B:302	BINDING SITE FOR RESIDUE CD B 301
09	AC9	SOFTWARE	CYS B:65 , GLU B:92 , ASP B:116 , CD B:301 , CL B:303 , HOH B:403 , HOH B:404	BINDING SITE FOR RESIDUE CD B 302
10	BC1	SOFTWARE	CYS B:65 , GLU B:92 , ASP B:116 , ASN B:120 , CD B:302	BINDING SITE FOR RESIDUE CL B 303
11	BC2	SOFTWARE	LYS B:71 , ARG B:166 , GLU B:170 , HIS B:171 , LEU B:172 , HOH B:424	BINDING SITE FOR RESIDUE SO4 B 304
12	BC3	SOFTWARE	ARG A:127 , HOH A:1143 , THR B:66 , HIS B:67 , LYS B:159	BINDING SITE FOR RESIDUE SO4 B 305
13	BC4	SOFTWARE	GLY B:123 , ALA B:124 , THR B:125 , ARG B:187 , HOH B:420 , HOH B:445	BINDING SITE FOR RESIDUE SO4 B 306
14	BC5	SOFTWARE	HIS A:185 , GLY A:197 , GLU A:198 , ARG B:107 , PRO B:109 , ILE B:204 , ASP B:207	BINDING SITE FOR RESIDUE MMJ B 307

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

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:133
 aligned with Q72498_9HIV1 | Q72498 from UniProtKB/TrEMBL  Length:1003

    Alignment length:151
                                   781       791       801       811       821       831       841       851       861       871       881       891       901       911       921 
         Q72498_9HIV1   772 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATD 922
               SCOP domains d3vq5a_ A: Retroviral integrase, catalytic domain                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh.ee.-------------.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.-----..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vq5 A  57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTGATVRAACDWAGIKQE-------------ESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKR-----GYSAGERIVDIIATD 207
                                    66        76        86        96       106       116       126       136 |       -     | 156       166       176       186|     |196       206 
                                                                                                           138           152                                187   193

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with Q72498_9HIV1 | Q72498 from UniProtKB/TrEMBL  Length:1003

    Alignment length:151
                                   781       791       801       811       821       831       841       851       861       871       881       891       901       911       921 
         Q72498_9HIV1   772 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATD 922
               SCOP domains d3vq5b_ B: Retroviral integrase, catalytic domain                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh.ee.--------------.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.-----..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vq5 B  57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTGATVRAACDWAGIKQE--------------SMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKR-----GYSAGERIVDIIATD 207
                                    66        76        86        96       106       116       126       136 |       -      |156       166       176       186|     |196       206 
                                                                                                           138            153                               187   193

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q72498_9HIV1 | Q72498)

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: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.

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	3vq5
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)