4EDGA

The structure of the s. aureus dnag rna polymerase domain bound to atp and manganese
Total Genus 119
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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
119
sequence length
321
structure length
321
Chain Sequence
SNADDLQMIEMHELIQEFYYYALTKTVEGEQALTYLQERGFTDALIKERGIGFAPDSSHFCHDFLQKKGYDIELAYEAGLLSRNEENFSYYDRFRNRIMFPLKNAQGRIVGYSGRTYTGQEPKYLNSPETPIFQKRKLLYNLDKARKSIRKLDEIVLLEGFMDVIKSDTAGLKNVVATMGTQLSDEHITFIRKLTSNITLMFDGDFAGSEATLKTGQHLLQQGLNVFVIQLPSGMDPDEYIGKYGNDAFTTFVKNDKKSFAHYKVSILKDEIAHNDLSYERYLKELSHDISLMKSSILQQKAINDVAPFFNVSPEQLANEI
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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 Binding Mechanism of Metal-NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases.
pubmed doi rcsb
source organism Staphylococcus aureus
molecule tags Transferase
total genus 119
structure length 321
sequence length 321
ec nomenclature ec 2.7.7.-:
pdb deposition date 2012-03-27

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF08275 Toprim_N DNA primase catalytic core, N-terminal domain
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 4edgA03
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 4edgA02
3.90.980.10 Alpha Beta Alpha-Beta Complex DNA primase DNAg catalytic core, N-terminal domain DNA primase, catalytic core, N-terminal domain 4edgA01
5GUJA 1T6T1 3VDPA 2Q2EA 4O6PB 1DD9A 4EDGA 4EDVA 4EDKA 4EDTA 2V1CA 3B39A 2AU3A 4EE1A 3VDUA 4O6OA 3VE5A 1DDEA 1D3YA 2ZBKA 4JCVA 1EQNA 1VDDA 4EDRA 4E2KA
chains in the Genus database with same CATH superfamily
2NSWA 5GUJA 1T6T1 3VDPA 1ERCA 2Q2EA 3KLSA 4O6PB 1DD9A 4EDGA 4EDVA 4EDKA 4EDTA 3CU7A 3B39A 2V1CA 2AU3A 4EE1A 3VDUA 2I5RA 4O6OA 3VE5A 2NSVA 1DDEA 3KXRA 1D3YA 2JMSA 2B39A 2KK2A 2ZBKA 4JCVA 2KC6A 2LMKA 1EQNA 1VDDA 4EDRA 2ERLA 2FCJA 4E2KA
chains in the Genus database with same CATH topology
2NSWA 5GUJA 1T6T1 3VDPA 1ERCA 2Q2EA 3KLSA 4O6PB 1DD9A 4EDGA 4EDVA 4EDKA 4EDTA 3CU7A 3B39A 2V1CA 2AU3A 4EE1A 3VDUA 4O6OA 3VE5A 2NSVA 1DDEA 3KXRA 1D3YA 2JMSA 2B39A 2KK2A 2ZBKA 4JCVA 2KC6A 2LMKA 1EQNA 1VDDA 4EDRA 2ERLA 4E2KA
chains in the Genus database with same CATH homology


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