1ZDEA

1.95 angstrom crystal structure of a dnae intein precursor from synechocystis sp. pcc 6803
Total Genus 40
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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
40
sequence length
170
structure length
160
Chain Sequence
AMEKFAEYALSFGTEILTVEYGPLPIGKIVSEEINCSVYSVDPEGRVYTQAIAQWHDRGEQEVLEYELEDGSVIRATSDHRFLTTDYQLLAIEEIFARQLDLLTLENHRLPFPLLDAGTIKMVKVIGRRSLGVQRIFDIGLPQDHNFLLANGAIAAACFN
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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 Crystal structures of an intein from the split dnaE gene of Synechocystis sp. PCC6803 reveal the catalytic model without the penultimate histidine and the mechanism of zinc ion inhibition of protein splicing
pubmed doi rcsb
molecule tags Transferase
source organism Synechocystis sp. pcc 6803
molecule keywords DNA polymerase III alpha subunit
total genus 40
structure length 160
sequence length 170
ec nomenclature ec 2.7.7.7: DNA-directed DNA polymerase.
pdb deposition date 2005-04-14
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.170.16.10 Mainly Beta Beta Complex Endonuclease - Pi-scei; Chain A, domain 1 Hedgehog/Intein (Hint) domain 1zdeA00
1EF0A 1ZDEA 5K08A 2LQMA 2LWYA 2CW7A 2CW8A 1GPPA 4O1SA 2LCJA 5I0AA 4KL6A 4KL5A 1ZD7A 4GIGA 1LWSA 1AT0A 4E2TA 2L8LA 2JNQA 1AM2A 2IN9A 2IMZA 2IN8A 2JMZA 4E2UA 3IGDA 3NZMA 4OZ6A 2IN0A 1VDEA 1DFAA 4O1RA 1DQ3A 2KEQA 3IFJA 1MI8A 1JVAA 1LWTA 1UM2A
chains in the Genus database with same CATH superfamily
1EF0A 1ZDEA 5K08A 4QFQA 2LQMA 2LWYA 2CW7A 2CW8A 1GPPA 4O1SA 2LCJA 5I0AA 4KL6A 4KL5A 1ZD7A 4GIGA 4LX3A 1AT0A 4E2TA 1LWSA 2L8LA 2JNQA 1AM2A 2IN9A 2IMZA 2IN8A 2JMZA 4E2UA 3IGDA 3NZMA 4OZ6A 2IN0A 1VDEA 1DFAA 4O1RA 1DQ3A 2KEQA 3IFJA 1MI8A 1JVAA 1LWTA 1UM2A
chains in the Genus database with same CATH topology
1EF0A 1ZDEA 5K08A 2LQMA 2LWYA 2CW7A 2CW8A 1GPPA 4O1SA 2LCJA 5I0AA 4KL6A 4KL5A 1ZD7A 4GIGA 1LWSA 1AT0A 4E2TA 2L8LA 2JNQA 1AM2A 2IN9A 2IMZA 2IN8A 2JMZA 4E2UA 3IGDA 3NZMA 4OZ6A 2IN0A 1VDEA 1DFAA 4O1RA 1DQ3A 2KEQA 3IFJA 1MI8A 1JVAA 1LWTA 1UM2A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1EF0 A;  1ZDE A;  5K08 A;  2LQM A;  2LWY A;  2CW7 A;  2CW8 A;  1GPP A;  4O1S A;  2LCJ A;  5I0A A;  4KL6 A;  4KL5 A;  1ZD7 A;  4GIG A;  1LWS A;  1AT0 A;  4E2T A;  2L8L A;  2JNQ A;  1AM2 A;  2IN9 A;  2IMZ A;  2IN8 A;  2JMZ A;  4E2U A;  3IGD A;  3NZM A;  4OZ6 A;  2IN0 A;  1VDE A;  1DFA A;  4O1R A;  1DQ3 A;  2KEQ A;  3IFJ A;  1MI8 A;  1JVA A;  1LWT A;  1UM2 A; 
#chains in the Genus database with same CATH topology
 1EF0 A;  1ZDE A;  5K08 A;  4QFQ A;  2LQM A;  2LWY A;  2CW7 A;  2CW8 A;  1GPP A;  4O1S A;  2LCJ A;  5I0A A;  4KL6 A;  4KL5 A;  1ZD7 A;  4GIG A;  4LX3 A;  1AT0 A;  4E2T A;  1LWS A;  2L8L A;  2JNQ A;  1AM2 A;  2IN9 A;  2IMZ A;  2IN8 A;  2JMZ A;  4E2U A;  3IGD A;  3NZM A;  4OZ6 A;  2IN0 A;  1VDE A;  1DFA A;  4O1R A;  1DQ3 A;  2KEQ A;  3IFJ A;  1MI8 A;  1JVA A;  1LWT A;  1UM2 A; 
#chains in the Genus database with same CATH homology
 1EF0 A;  1ZDE A;  5K08 A;  2LQM A;  2LWY A;  2CW7 A;  2CW8 A;  1GPP A;  4O1S A;  2LCJ A;  5I0A A;  4KL6 A;  4KL5 A;  1ZD7 A;  4GIG A;  1LWS A;  1AT0 A;  4E2T A;  2L8L A;  2JNQ A;  1AM2 A;  2IN9 A;  2IMZ A;  2IN8 A;  2JMZ A;  4E2U A;  3IGD A;  3NZM A;  4OZ6 A;  2IN0 A;  1VDE A;  1DFA A;  4O1R A;  1DQ3 A;  2KEQ A;  3IFJ A;  1MI8 A;  1JVA A;  1LWT A;  1UM2 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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