4EDKA

The structure of the s. aureus dnag rna polymerase domain bound to gtp and manganese
Total Genus 115
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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
115
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 115
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 4edkA03
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 4edkA02
3.90.980.10 Alpha Beta Alpha-Beta Complex DNA primase DNAg catalytic core, N-terminal domain DNA primase, catalytic core, N-terminal domain 4edkA01
2V1CA 1T6T1 3VDPA 2Q2EA 5GUJA 4EE1A 4EDKA 3B39A 3VDUA 2ZBKA 1VDDA 1DD9A 4EDGA 1EQNA 4E2KA 4O6OA 4EDTA 4JCVA 1D3YA 4O6PB 4EDRA 3VE5A 1DDEA 4EDVA 2AU3A
chains in the Genus database with same CATH superfamily
2KK2A 2V1CA 1T6T1 2JMSA 3VDPA 2Q2EA 5GUJA 2ERLA 4EE1A 4EDKA 3B39A 3VDUA 2ZBKA 1VDDA 3CU7A 1DD9A 2NSWA 3KLSA 4EDGA 1EQNA 2KC6A 4E2KA 4O6OA 4EDTA 2LMKA 2FCJA 1D3YA 4JCVA 4O6PB 4EDRA 2B39A 3VE5A 1DDEA 3KXRA 4EDVA 1ERCA 2AU3A 2I5RA 2NSVA
chains in the Genus database with same CATH topology
2KK2A 2V1CA 1T6T1 2JMSA 3VDPA 2Q2EA 5GUJA 2ERLA 4EE1A 4EDKA 3B39A 3VDUA 2ZBKA 1VDDA 3CU7A 1DD9A 2NSWA 3KLSA 4EDGA 1EQNA 2KC6A 4E2KA 4O6OA 4EDTA 2LMKA 1D3YA 4JCVA 4O6PB 4EDRA 2B39A 3VE5A 1DDEA 3KXRA 4EDVA 1ERCA 2AU3A 2NSVA
chains in the Genus database with same CATH homology


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