4EDVA

The structure of the s. aureus dnag rna polymerase domain bound to pppgpp and manganese
Total Genus 121
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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
121
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/transferase inhibitor
source organism Staphylococcus aureus
molecule keywords DNA primase
total genus 121
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 4edvA03
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 4edvA02
3.90.980.10 Alpha Beta Alpha-Beta Complex DNA primase DNAg catalytic core, N-terminal domain DNA primase, catalytic core, N-terminal domain 4edvA01
2ZBKA 4EE1A 2V1CA 4O6OA 1T6T1 2AU3A 4EDRA 4EDVA 4EDGA 4EDKA 5GUJA 3VE5A 4JCVA 4EDTA 3B39A 4O6PB 1D3YA 1VDDA 4E2KA 1EQNA 1DDEA 3VDPA 2Q2EA 1DD9A 3VDUA
chains in the Genus database with same CATH superfamily
2ZBKA 4EE1A 3CU7A 2V1CA 3KXRA 4O6OA 1T6T1 2AU3A 2KK2A 2JMSA 4EDRA 2B39A 2LMKA 2FCJA 2ERLA 4EDVA 4EDKA 2NSVA 4EDGA 5GUJA 3VE5A 2KC6A 2I5RA 4JCVA 4EDTA 3B39A 2NSWA 4O6PB 1ERCA 3KLSA 1D3YA 1VDDA 4E2KA 1EQNA 1DDEA 3VDPA 2Q2EA 1DD9A 3VDUA
chains in the Genus database with same CATH topology
2ZBKA 4EE1A 3CU7A 2V1CA 3KXRA 4O6OA 1T6T1 2AU3A 2KK2A 2JMSA 4EDRA 2B39A 2LMKA 2ERLA 4EDVA 4EDKA 2NSVA 4EDGA 5GUJA 3VE5A 2KC6A 4JCVA 4EDTA 3B39A 2NSWA 4O6PB 1ERCA 3KLSA 1D3YA 1VDDA 4E2KA 1EQNA 1DDEA 3VDPA 2Q2EA 1DD9A 3VDUA
chains in the Genus database with same CATH homology


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