4LIMA

Crystal structure of the catalytic subunit of yeast primase
Total Genus 143
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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
143
sequence length
388
structure length
381
Chain Sequence
GANGPSSSDMEYYYKSLYPFKHIFNWLNHSPKPSRDMINREFAMAFRSGAYKRYNSFNSVQDFKAQIEKANPDRFEIGAIYNKPPREELKALEKELVFDIDMDDYDAFRTCCSGAQVCSKCWKFISLAMKITNTALREDFGYKDFIWVFSGRRGAHCWVSDKRARALTDVQRRNVLDYVNVIRDRNTDKRLALKRPYHPHLARSLEQLKPFFVSIMLEEQNPWEDDQHAIQTLLPALYDKQLIDSLKKYWLDNPRRSSKEKWNDIDQIATSLFKGPKQDSHIIKLRECKEDLVLMTLYPKLDVEVTKQTIHLLKAPFCIHPATGNVCVPIDESFAPEKAPKLIDLQTEMEKNNDVSLTALQPFINQFQAYVSSLLKNELGS
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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 Insights into Eukaryotic Primer Synthesis from Structures of the p48 Subunit of Human DNA Primase.
pubmed doi rcsb
molecule tags Transferase
source organism Saccharomyces cerevisiae
molecule keywords DNA primase small subunit
total genus 143
structure length 381
sequence length 388
ec nomenclature ec 2.7.7.-:
pdb deposition date 2013-07-02

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01896 DNA_primase_S DNA primase small subunit
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.920.30 Alpha Beta Alpha-Beta Complex DNA primase, PRIM domain DNA primase, PRIM domain 4limA00
4BPUA 1ZT2A 4MM2A 4BPXA 4MHQA 2FAQA 2FARA 4LIMA 2FAOA 4LILA 4RR2A 4LIKA 5EXRA 4BPWA
chains in the Genus database with same CATH superfamily
1V33A 4BPUA 1ZT2A 4MM2A 1G71A 4BPXA 4MHQA 5EXRA 4LIKA 2FAQA 2FARA 4LIMA 2FAOA 4LILA 4RR2A 2ATZA 1V34A 4BPWA
chains in the Genus database with same CATH topology
1V33A 4BPUA 1ZT2A 4MM2A 1G71A 4BPXA 4MHQA 5EXRA 2FAQA 2FARA 4LIMA 2FAOA 4LILA 4RR2A 4LIKA 1V34A 4BPWA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4BPU A;  1ZT2 A;  4MM2 A;  4BPX A;  4MHQ A;  2FAQ A;  2FAR A;  4LIM A;  2FAO A;  4LIL A;  4RR2 A;  4LIK A;  5EXR A;  4BPW A; 
#chains in the Genus database with same CATH topology
 1V33 A;  4BPU A;  1ZT2 A;  4MM2 A;  1G71 A;  4BPX A;  4MHQ A;  5EXR A;  4LIK A;  2FAQ A;  2FAR A;  4LIM A;  2FAO A;  4LIL A;  4RR2 A;  2ATZ A;  1V34 A;  4BPW A; 
#chains in the Genus database with same CATH homology
 1V33 A;  4BPU A;  1ZT2 A;  4MM2 A;  1G71 A;  4BPX A;  4MHQ A;  5EXR A;  2FAQ A;  2FAR A;  4LIM A;  2FAO A;  4LIL A;  4RR2 A;  4LIK A;  1V34 A;  4BPW 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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#similar chains in the pdb database (?% sequence similarity)
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