3B39A

Structure of the dnag primase catalytic domain bound to ssdna
Total Genus 92
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
92
sequence length
319
structure length
317
Chain Sequence
NAHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWCALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDSQL
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title Identification of a DNA primase template tracking site redefines the geometry of primer synthesis.
pubmed doi rcsb
molecule tags Transferase/dna
source organism Escherichia coli
molecule keywords DNA (5'-D(*DCP*DAP*DAP*DAP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DGP*D
total genus 92
structure length 317
sequence length 319
chains with identical sequence B
ec nomenclature ec 2.7.7.-:
pdb deposition date 2007-10-19

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF08275 Toprim_N DNA primase catalytic core, N-terminal domain
A PF10410 DnaB_bind DnaB-helicase binding domain of primase
A PF13155 Toprim_2 Toprim-like
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.20.50.20 Mainly Alpha Up-down Bundle Pheromone ER-1 Pheromone ER-1 3b39A03
3.40.1360.10 Alpha Beta 3-Layer(aba) Sandwich Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 3b39A02
3.90.980.10 Alpha Beta Alpha-Beta Complex DNA primase DNAg catalytic core, N-terminal domain DNA primase, catalytic core, N-terminal domain 3b39A01
4EDVA 5GUJA 3VDUA 2AU3A 4O6PB 3B39A 3VDPA 1DDEA 1EQNA 1D3YA 2V1CA 4EDRA 4EDTA 4JCVA 2ZBKA 2Q2EA 4E2KA 4EDKA 4O6OA 3VE5A 1VDDA 1T6T1 4EE1A 4EDGA 1DD9A
chains in the Genus database with same CATH superfamily
2LMKA 4EDVA 5GUJA 3VDUA 2AU3A 3CU7A 2KK2A 4O6PB 3B39A 2NSWA 3VDPA 3KXRA 1DDEA 1EQNA 1D3YA 2V1CA 2B39A 3KLSA 4EDRA 4EDTA 2JMSA 2I5RA 4JCVA 2ZBKA 2FCJA 2Q2EA 2ERLA 1ERCA 4E2KA 4EDKA 4O6OA 3VE5A 2KC6A 1VDDA 1T6T1 2NSVA 4EE1A 4EDGA 1DD9A
chains in the Genus database with same CATH topology
2LMKA 4EDVA 5GUJA 3VDUA 2AU3A 3CU7A 2KK2A 4O6PB 3B39A 2NSWA 3VDPA 3KXRA 1DDEA 1EQNA 1D3YA 2V1CA 2B39A 3KLSA 4EDRA 4EDTA 2JMSA 4JCVA 2ZBKA 2Q2EA 2ERLA 1ERCA 4E2KA 4EDKA 4O6OA 3VE5A 2KC6A 1VDDA 1T6T1 2NSVA 4EE1A 4EDGA 1DD9A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4EDV A;  5GUJ A;  3VDU A;  2AU3 A;  4O6P B;  3B39 A;  3VDP A;  1DDE A;  1EQN A;  1D3Y A;  2V1C A;  4EDR A;  4EDT A;  4JCV A;  2ZBK A;  2Q2E A;  4E2K A;  4EDK A;  4O6O A;  3VE5 A;  1VDD A;  1T6T 1;  4EE1 A;  4EDG A;  1DD9 A; 
#chains in the Genus database with same CATH topology
 2LMK A;  4EDV A;  5GUJ A;  3VDU A;  2AU3 A;  3CU7 A;  2KK2 A;  4O6P B;  3B39 A;  2NSW A;  3VDP A;  3KXR A;  1DDE A;  1EQN A;  1D3Y A;  2V1C A;  2B39 A;  3KLS A;  4EDR A;  4EDT A;  2JMS A;  2I5R A;  4JCV A;  2ZBK A;  2FCJ A;  2Q2E A;  2ERL A;  1ERC A;  4E2K A;  4EDK A;  4O6O A;  3VE5 A;  2KC6 A;  1VDD A;  1T6T 1;  2NSV A;  4EE1 A;  4EDG A;  1DD9 A; 
#chains in the Genus database with same CATH homology
 2LMK A;  4EDV A;  5GUJ A;  3VDU A;  2AU3 A;  3CU7 A;  2KK2 A;  4O6P B;  3B39 A;  2NSW A;  3VDP A;  3KXR A;  1DDE A;  1EQN A;  1D3Y A;  2V1C A;  2B39 A;  3KLS A;  4EDR A;  4EDT A;  2JMS A;  4JCV A;  2ZBK A;  2Q2E A;  2ERL A;  1ERC A;  4E2K A;  4EDK A;  4O6O A;  3VE5 A;  2KC6 A;  1VDD A;  1T6T 1;  2NSV A;  4EE1 A;  4EDG A;  1DD9 A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
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