4EDRA

The structure of the s. aureus dnag rna polymerase domain bound to utp and manganese
Total Genus 114
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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
114
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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publication title Binding Mechanism of Metal-NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases.
pubmed doi rcsb
molecule tags Transferase
source organism Staphylococcus aureus
molecule keywords DNA primase
total genus 114
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 4edrA03
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 4edrA02
3.90.980.10 Alpha Beta Alpha-Beta Complex DNA primase DNAg catalytic core, N-terminal domain DNA primase, catalytic core, N-terminal domain 4edrA01
4EDGA 2V1CA 4EDKA 4EE1A 2ZBKA 3B39A 4O6PB 2AU3A 4EDTA 4O6OA 1EQNA 3VE5A 4JCVA 5GUJA 1DD9A 4EDVA 4EDRA 1VDDA 1T6T1 3VDUA 3VDPA 1D3YA 1DDEA 2Q2EA 4E2KA
chains in the Genus database with same CATH superfamily
4EDGA 2FCJA 2V1CA 2KC6A 4EDKA 4EE1A 2ZBKA 3B39A 4O6PB 2AU3A 4EDTA 4O6OA 2NSWA 2ERLA 1EQNA 3VE5A 2NSVA 2I5RA 4JCVA 5GUJA 1ERCA 2B39A 1DD9A 4EDVA 3KXRA 3CU7A 4EDRA 3KLSA 1VDDA 2LMKA 1T6T1 3VDUA 2JMSA 3VDPA 2KK2A 1DDEA 1D3YA 2Q2EA 4E2KA
chains in the Genus database with same CATH topology
4EDGA 2V1CA 2KC6A 4EDKA 4EE1A 2ZBKA 3B39A 4O6PB 2AU3A 4EDTA 4O6OA 2NSWA 2ERLA 1EQNA 3VE5A 2NSVA 4JCVA 5GUJA 1ERCA 2B39A 1DD9A 4EDVA 3KXRA 3CU7A 4EDRA 3KLSA 1VDDA 2LMKA 1T6T1 3VDUA 2JMSA 3VDPA 2KK2A 1DDEA 1D3YA 2Q2EA 4E2KA
chains in the Genus database with same CATH homology


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