4EDGA

The structure of the s. aureus dnag rna polymerase domain bound to atp and manganese
Total Genus 119

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
5010015020025030030025020015010050
020406080100Genus Matrix

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
3H1 (134-136)AH1 (109-132)AH5 (179-185)EMPTYAH2 (137-146)AH3 (150-156)TI1 (192-195)AH6 (249-259)S3 (196-199)TVIII1 (199-202)S1 (159-161)TIV3 (201-204)AH4 (167-175)TI3 (237-240)TIV1 (164-167)TI2 (211-214)S2 (188-191)S5 (216-222)TIV2 (191-194)TIV5 (227-230)S4 (204-210)S7 (262-264)TIV4 (223-226)S6 (231-233)TI4 (241-244)TI5 (242-245)AH7 (268-277)TIV7 (285-288)S8 (282-283)TIV6 (279-282)AH8 (292-301)S9 (304-307)TII1 (246-249)AH9 (313-329)Updating...
connected with : NaN
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 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 4edgA03
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 4edgA02
3.90.980.10 Alpha Beta Alpha-Beta Complex DNA primase DNAg catalytic core, N-terminal domain DNA primase, catalytic core, N-terminal domain 4edgA01
4EDVA 4EE1A 3B39A 2V1CA 2ZBKA 4EDKA 1DDEA 4JCVA 1T6T1 2AU3A 4EDRA 4O6OA 4EDGA 1VDDA 3VE5A 2Q2EA 3VDUA 1DD9A 3VDPA 5GUJA 4EDTA 1D3YA 1EQNA 4E2KA 4O6PB
chains in the Genus database with same CATH superfamily
2ERLA 4EDVA 4EE1A 1ERCA 3B39A 2V1CA 2JMSA 2FCJA 2ZBKA 4EDKA 1DDEA 2NSWA 4JCVA 1T6T1 2B39A 2AU3A 4EDRA 2LMKA 4O6OA 4EDGA 3KXRA 1VDDA 3CU7A 3VE5A 2I5RA 2Q2EA 3VDUA 2NSVA 1DD9A 3VDPA 5GUJA 4EDTA 2KK2A 2KC6A 1D3YA 3KLSA 1EQNA 4E2KA 4O6PB
chains in the Genus database with same CATH topology
2ERLA 4EDVA 4EE1A 1ERCA 3B39A 2V1CA 2JMSA 2ZBKA 4EDKA 1DDEA 2NSWA 4JCVA 1T6T1 2B39A 2AU3A 4EDRA 2LMKA 4O6OA 4EDGA 3KXRA 1VDDA 3CU7A 3VE5A 2Q2EA 3VDUA 2NSVA 1DD9A 3VDPA 5GUJA 4EDTA 2KK2A 2KC6A 1D3YA 3KLSA 1EQNA 4E2KA 4O6PB
chains in the Genus database with same CATH homology


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

 
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#similar chains, but unknotted
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