4EDTA

The structure of the s. aureus dnag rna polymerase domain bound to ppgpp 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/transferase inhibitor
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 4edtA03
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 4edtA02
3.90.980.10 Alpha Beta Alpha-Beta Complex DNA primase DNAg catalytic core, N-terminal domain DNA primase, catalytic core, N-terminal domain 4edtA01
4EDKA 4EDRA 1T6T1 1DDEA 1EQNA 1VDDA 3VE5A 3VDPA 4EDVA 1D3YA 4O6PB 4EDGA 4EE1A 2Q2EA 4E2KA 2AU3A 4O6OA 4JCVA 5GUJA 2ZBKA 3VDUA 2V1CA 4EDTA 1DD9A 3B39A
chains in the Genus database with same CATH superfamily
1ERCA 4EDKA 2B39A 4EDRA 1T6T1 1DDEA 3KLSA 2NSWA 1EQNA 1VDDA 3VE5A 3VDPA 2KK2A 4EDVA 1D3YA 2NSVA 3CU7A 4O6PB 4EDGA 4EE1A 2FCJA 2LMKA 2Q2EA 4E2KA 2AU3A 4O6OA 2I5RA 2ERLA 4JCVA 2JMSA 5GUJA 2ZBKA 3VDUA 2V1CA 4EDTA 1DD9A 3KXRA 2KC6A 3B39A
chains in the Genus database with same CATH topology
1ERCA 4EDKA 2B39A 4EDRA 1T6T1 1DDEA 3KLSA 2NSWA 1EQNA 1VDDA 3VE5A 3VDPA 2KK2A 4EDVA 1D3YA 2NSVA 3CU7A 4O6PB 4EDGA 4EE1A 2LMKA 2Q2EA 4E2KA 2AU3A 4O6OA 2ERLA 4JCVA 2JMSA 5GUJA 2ZBKA 3VDUA 2V1CA 4EDTA 1DD9A 3KXRA 2KC6A 3B39A
chains in the Genus database with same CATH homology


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