1KC6 | PD0272 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   HINCII BOUND TO COGNATE DNA

Authors :   N. C. Horton, L. F. Dorner, J. J. Perona

Date :   07 Nov 01 (Deposition) - 07 Dec 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,E,F  (1x)
Biol. Unit 2: C,D,G,H  (1x)

Keywords :   Restriction Endonuclease, Blunt Cutting, Protein-Dna, Indirect Readout, Dna Bending, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. C. Horton, L. F. Dorner, J. J. Perona
Sequence Selectivity And Degeneracy Of A Restriction Endonuclease Mediated By Dna Intercalation.
Nat. Struct. Biol. V. 9 42 2002
PubMed-ID: 11742344 | Reference-DOI: 10.1038/NSB741
(for further references see the PDB file header)

*Molecule 1 - 5'-D(PCPCPGPGPTPCPGPAPCPCPGPG)-3'*
	Chains	:	E, F, G, H
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - TYPE II RESTRICTION ENZYME HINCII
	Chains	:	A, B, C, D
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	ENDONUCLEASE HINCII

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B			E	F
Biological Unit 2 (1x)	:			C	D			G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:127 , ILE A:142 , HOH A:756 , HOH A:757 , DC F:7 , DG F:8	BINDING SITE FOR RESIDUE NA A 701
2	AC2	SOFTWARE	ASP B:127 , ILE B:142 , HOH B:375 , DC E:7 , DG E:8 , HOH E:435	BINDING SITE FOR RESIDUE NA E 702

(no "SS Bond" information available for 1KC6)

(no "Cis Peptide Bond" information available for 1KC6)

(no "SAP(SNP)/Variant" information available for 1KC6)

(no "PROSITE Motif" information available for 1KC6)

(no "Exon" information available for 1KC6)

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:249
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
               SCOP domains d1kc6a_ A: Restriction         endonuclease HincII                                                                                                                                                                                                                SCOP domains
               CATH domains 1kc6A00 A:2-258  [code        =3.40.600.10, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eee..--------..hhhhhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhh...............eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhhh....eeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhheee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kc6 A   2 SFIKPIYQDINSILIGQKVKRP--------AAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
                                    11        21 |       -|       41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
                                                23       32

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
               SCOP domains d1kc6b_ B: Restrictio         n endonuclease HincII                                                                                                                                                                                                              SCOP domains
               CATH domains 1kc6B00 B:2-257  [cod         e=3.40.600.10, no name defined]                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eee.---------...hhhhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhh..hhhhhhhhh.hhhhhhhh...............eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeeeee...eeeeeeeeeee.hhhhhhhheee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kc6 B   2 SFIKPIYQDINSILIGQKVKR---------AAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11        21|        -|       41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
                                               22        32

Chain C from PDB  Type:PROTEIN  Length:233
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
               SCOP domains d1kc6c_ C: Restricti           on endonuclease HincII                                                                                                                                                                                                            SCOP domains
               CATH domains 1kc6C00 C:2-257  [co           de=3.40.600.10, no name defined]                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..ee.-----------.hhhhhhhhhhhhhhhhhh.ee.hhhhhhhhh--------.hhhhhhh.hhhhhhhhh...........---..........eeee.-..eeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeee.hhh.....eee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kc6 C   2 SFIKPIYQDINSILIGQKVK-----------AGEPFEKLVYKFLKENLSDLTFKQYEYLNDLF--------HEARYKLFNSPTLLFLLSRGKAATENWSI---FEEKQNDTADILLVK-QFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11        21         - |      41        51        61  |      - |      81        91       101   |   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
                                              21          33                             64       73                         101 105           119 |                                                                                                                                        
                                                                                                                                                 121

Chain D from PDB  Type:PROTEIN  Length:236
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
               SCOP domains d1kc6d_ D: Restric              tion endonuclease HincII                                                                                                                                                                                                         SCOP domains
               CATH domains 1kc6D00 D:2-257  [              code=3.40.600.10, no name defined]                                                                                                                                                                                               CATH domains
           Pfam domains (1) Endonuc-HincII-1kc              6D01 D:2-257                                                                                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) Endonuc-HincII-1kc              6D02 D:2-257                                                                                                                                                                                                                     Pfam domains (2)
           Pfam domains (3) Endonuc-HincII-1kc              6D03 D:2-257                                                                                                                                                                                                                     Pfam domains (3)
           Pfam domains (4) Endonuc-HincII-1kc              6D04 D:2-257                                                                                                                                                                                                                     Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhh...--------------hhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.....hhhhhhh...hhhhhhhhh.hhhhhhhh...............eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeee------....eeeeee.hhh.....eee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kc6 D   2 SFIKPIYQDINSILIGQK--------------GEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDW------LVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11       | -         -  |     41        51        61        71        81        91       101       111       121       131       141       151       161       171 |     181       191       201       211       221       231       241       251      
                                            19             34                                                                                                                                        173    180

Chain E from PDB  Type:DNA  Length:12
                                            
                 1kc6 E   2 CCGGTCGACCGG  13
                                    11

Chain F from PDB  Type:DNA  Length:12
                                            
                 1kc6 F   2 CCGGTCGACCGG  13
                                    11

Chain G from PDB  Type:DNA  Length:12
                                            
                 1kc6 G   2 CCGGTCGACCGG  13
                                    11

Chain H from PDB  Type:DNA  Length:12
                                            
                 1kc6 H   2 CCGGTCGACCGG  13
                                    11

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

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: Restriction endonuclease HincII (19)

Protein domain: Restriction endonuclease HincII (19)

Haemophilus influenzae [TaxId: 727] (19)

1a	d1kc6a_	A:
1b	d1kc6b_	B:
1c	d1kc6c_	C:
1d	d1kc6d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: ECO RV Endonuclease; Chain A (56)

Homologous Superfamily: [code=3.40.600.10, no name defined] (55)

[unclassified] (40)

1a	1kc6D00	D:2-257
1b	1kc6C00	C:2-257
1c	1kc6B00	B:2-257
1d	1kc6A00	A:2-258

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Endonuc-HincII] (3)

Family: Endonuc-HincII (3)

Haemophilus influenzae (2)

1a	Endonuc-HincII-1kc6D01	D:2-257
1b	Endonuc-HincII-1kc6D02	D:2-257
1c	Endonuc-HincII-1kc6D03	D:2-257
1d	Endonuc-HincII-1kc6D04	D:2-257

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (T2C2_HAEIF | P17743)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0009307	DNA restriction-modification system	A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

Asymmetric Unit
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Biological Units
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	1kc6
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(no "Related Entries Specified in the PDB File" available for 1KC6)

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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