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
1DQ3A 1MI8A 2L8LA 2CW7A 2IN8A 3NZMA 1LWTA 4KL6A 5I0AA 1DFAA 1UM2A 1EF0A 1LWSA 2LQMA 1AT0A 1VDEA 2IMZA 4KL5A 4O1SA 1JVAA 2JNQA 3IFJA 1ZDEA 4OZ6A 2CW8A 4E2UA 4E2TA 2LCJA 2IN9A 4O1RA 4GIGA 1ZD7A 2IN0A 2LWYA 2JMZA 2KEQA 3IGDA 5K08A 1AM2A 1GPPA
chains in the Genus database with same CATH superfamily
1DQ3A 1MI8A 2L8LA 4LX3A 2CW7A 4QFQA 2IN8A 3NZMA 1LWTA 4KL6A 5I0AA 1DFAA 1UM2A 1EF0A 1LWSA 2LQMA 1AT0A 1VDEA 2IMZA 4KL5A 4O1SA 1JVAA 2JNQA 3IFJA 1ZDEA 4OZ6A 2CW8A 4E2UA 4E2TA 2LCJA 2IN9A 4O1RA 4GIGA 1ZD7A 2IN0A 2LWYA 2JMZA 2KEQA 3IGDA 5K08A 1AM2A 1GPPA
chains in the Genus database with same CATH topology
1DQ3A 1MI8A 2L8LA 2CW7A 2IN8A 3NZMA 1LWTA 4KL6A 5I0AA 1DFAA 1UM2A 1EF0A 1LWSA 2LQMA 1AT0A 1VDEA 2IMZA 4KL5A 4O1SA 1JVAA 2JNQA 3IFJA 1ZDEA 4OZ6A 2CW8A 4E2UA 4E2TA 2LCJA 2IN9A 4O1RA 4GIGA 1ZD7A 2IN0A 2LWYA 2JMZA 2KEQA 3IGDA 5K08A 1AM2A 1GPPA
chains in the Genus database with same CATH homology


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

 
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#similar chains, but unknotted
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