1DDEA

Structure of the dnag catalytic core
Total Genus 101
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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
101
sequence length
313
structure length
310
Chain Sequence
TLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDSQL
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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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molecule keywords DNA PRIMASE
publication title Structure of the RNA polymerase domain of E. coli primase.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Transferase
total genus 101
structure length 310
sequence length 313
ec nomenclature ec 2.7.7.-:
pdb deposition date 1999-11-09

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 1ddeA03
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 1ddeA02
3.90.980.10 Alpha Beta Alpha-Beta Complex DNA primase DNAg catalytic core, N-terminal domain DNA primase, catalytic core, N-terminal domain 1ddeA01
5GUJA 2Q2EA 4EDRA 4EDGA 4O6PB 4EDTA 4O6OA 4EE1A 4E2KA 4EDVA 3VDUA 1EQNA 1DDEA 1VDDA 1DD9A 1D3YA 1T6T1 3B39A 3VE5A 4EDKA 2ZBKA 4JCVA 3VDPA 2AU3A 2V1CA
chains in the Genus database with same CATH superfamily
5GUJA 2LMKA 2Q2EA 2JMSA 4EDRA 2NSVA 2KK2A 4EDGA 1ERCA 4O6PB 3KXRA 3CU7A 4EDTA 4O6OA 4EE1A 4E2KA 4EDVA 2B39A 2NSWA 2KC6A 3VDUA 1EQNA 1DDEA 1VDDA 1DD9A 1D3YA 1T6T1 2ERLA 2FCJA 3B39A 3VE5A 3KLSA 2I5RA 4EDKA 2ZBKA 4JCVA 3VDPA 2AU3A 2V1CA
chains in the Genus database with same CATH topology
5GUJA 2LMKA 2Q2EA 2JMSA 4EDRA 2NSVA 2KK2A 4EDGA 1ERCA 4O6PB 3KXRA 3CU7A 4EDTA 4O6OA 4EE1A 4E2KA 4EDVA 2B39A 2NSWA 2KC6A 3VDUA 1EQNA 1DDEA 1VDDA 1DD9A 1D3YA 1T6T1 2ERLA 3B39A 3VE5A 3KLSA 4EDKA 2ZBKA 4JCVA 3VDPA 2AU3A 2V1CA
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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