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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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/transferase inhibitor
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
1T6T1 3B39A 1VDDA 5GUJA 2Q2EA 4EDGA 4O6OA 1DDEA 2ZBKA 1EQNA 4O6PB 3VE5A 4EDKA 3VDUA 4EDRA 1DD9A 4EDTA 4JCVA 2AU3A 2V1CA 1D3YA 4EE1A 4E2KA 4EDVA 3VDPA
chains in the Genus database with same CATH superfamily
1T6T1 3B39A 1VDDA 5GUJA 3KLSA 2Q2EA 4EDGA 1ERCA 2ERLA 4O6OA 1DDEA 2ZBKA 1EQNA 4O6PB 3VE5A 4EDKA 3VDUA 4EDRA 1DD9A 4EDTA 2NSWA 2JMSA 4JCVA 2AU3A 2V1CA 3CU7A 3KXRA 2KK2A 2LMKA 1D3YA 2NSVA 2I5RA 2KC6A 4EE1A 4E2KA 4EDVA 2FCJA 3VDPA 2B39A
chains in the Genus database with same CATH topology
1T6T1 3B39A 1VDDA 5GUJA 3KLSA 2Q2EA 4EDGA 1ERCA 2ERLA 4O6OA 1DDEA 2ZBKA 1EQNA 4O6PB 3VE5A 4EDKA 3VDUA 4EDRA 1DD9A 4EDTA 2NSWA 2JMSA 4JCVA 2AU3A 2V1CA 3CU7A 3KXRA 2KK2A 2LMKA 1D3YA 2NSVA 2KC6A 4EE1A 4E2KA 4EDVA 3VDPA 2B39A
chains in the Genus database with same CATH homology


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