1VYB - JenaLib

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:7 , ASN A:162 , LYS A:163 , LYS A:218 , ARG A:238 , HOH A:2215	BINDING SITE FOR RESIDUE SO4 A1239
02	AC2	SOFTWARE	ILE A:62 , TYR A:63 , GLN A:64 , ARG A:91 , HOH A:2216 , LYS B:85	BINDING SITE FOR RESIDUE SO4 A1240
03	AC3	SOFTWARE	GLY A:17 , LEU A:18 , ASN A:19 , HIS A:45 , HOH A:2217	BINDING SITE FOR RESIDUE SO4 A1241
04	AC4	SOFTWARE	LYS A:61 , TYR A:63 , PRO A:86 , HOH A:2218 , HOH A:2219 , TYR B:63 , PRO B:86	BINDING SITE FOR RESIDUE SO3 A1242
05	AC5	SOFTWARE	LYS A:68 , LYS A:93 , ALA B:21 , ARG B:24 , HIS B:25	BINDING SITE FOR RESIDUE SO4 B1239
06	AC6	SOFTWARE	GLY B:17 , LEU B:18 , ASN B:19 , HIS B:45 , HOH B:2070 , HOH B:2220	BINDING SITE FOR RESIDUE SO4 B1240
07	AC7	SOFTWARE	GLN A:159 , HIS B:7 , LYS B:218 , ARG B:238 , HOH B:2221 , HOH B:2222	BINDING SITE FOR RESIDUE SO4 B1241
08	AC8	SOFTWARE	GLN A:159 , LYS A:218 , LYS B:218 , ARG B:219 , HOH B:2223 , HOH B:2224	BINDING SITE FOR RESIDUE SO4 B1242
09	AC9	SOFTWARE	LYS B:71 , ALA B:72 , HIS B:96 , TYR B:115 , HOH B:2107 , HOH B:2225 , HOH B:2226 , HOH B:2227	BINDING SITE FOR RESIDUE SO3 B1243
10	BC1	SOFTWARE	THR A:224 , ASN A:225 , SER A:228 , HIS A:230 , SER A:231 , HOH A:2210 , HOH A:2220 , HOH A:2221 , TYR B:191 , TYR B:201	BINDING SITE FOR RESIDUE GOL A1243

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 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:236
 aligned with LORF2_HUMAN | O00370 from UniProtKB/Swiss-Prot  Length:1275

    Alignment length:236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      
          LORF2_HUMAN     3 GSNSHITILTLNVNGLNSPIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSILDRSTRQKVNKDTQELNSALHQTDLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELR 238
               SCOP domains d1vyba_ A: Endonuclease domain of LINE-1 reverse transcriptase homolog                                                                                                                                                                       SCOP domains
               CATH domains 1vybA00 A:3-238  [code=3.60.10.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.....hhhhhhhhhhhhhhhh..eeeee.......hhhhh......eeeee........eeeee......eeeeeee.....eeeeeeee..eeeeeeeee....hhhhhhhhhhhhh.......eeeeee.....hhhh.......hhhhhhhhhhhhhh.eeehhhhhh.......eee....eee..eeeeee.hhhh.eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vyb A   3 GSNSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELR 238
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with LORF2_HUMAN | O00370 from UniProtKB/Swiss-Prot  Length:1275

    Alignment length:233
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235   
          LORF2_HUMAN     6 SHITILTLNVNGLNSPIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSILDRSTRQKVNKDTQELNSALHQTDLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELR 238
               SCOP domains d1vybb_ B: Endonuclease domain of LINE-1 reverse transcriptase homolog                                                                                                                                                                    SCOP domains
               CATH domains 1vybB00 B:6-238  [code=3.60.10.10, no name defined]                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeee.......hhhhh......eeeee........eeeee.....eeeeeeee.....eeeeeeee..eeeeeeeee....hhhhhhhhhhhhh.......eeeeee.....hhhh.......hhhhhhhhhhhhhh.eeehhhhhh.......eee....eee..eeeeee.hhhh.eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vyb B   6 SHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELR 238
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235

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 (1, 2)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LORF2_HUMAN | O00370)

molecular function
	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:0009036	Type II site-specific deoxyribonuclease activity	Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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.
biological process
	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: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:0032199	reverse transcription involved in RNA-mediated transposition	The synthesis of DNA from an RNA transposon intermediate.
	GO:0032197	transposition, RNA-mediated	Any process involved in a type of transpositional recombination which occurs via an RNA intermediate.

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	Cis Peptide Bonds
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	1vyb
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)