3M4AA

Crystal structure of a bacterial topoisomerase ib in complex with dna reveals a secondary dna binding site
Total Genus 109
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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
109
sequence length
337
structure length
304
Chain Sequence
PSRTELLARRARIARLAVPPAYQDVYVSPDAENELQAFGRDAARLQYRYHPDFVALKKWQRLTRFAGALPTLKVATTADLRASGLPPRKVMALMTRLLHVARFRVGSDIYARQHKTYGLSTLRQRHVVVDGNTVTFRFKGKHGVSQHKATSDRTLAANMQKLLDLPGPWLFQTVDAGGERRRIHSTELNAYLREVIGPFTAKDFRTWGGTLLAAEYLAQQGTESSERQAKKVLVDCVKFVADDLGNTPAVTRGSYICPVIFDRYLDGKVLDDYEPRTERQEAELEGLTRSEGALKRMLESERTL
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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 structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site.
pubmed doi rcsb
molecule tags Isomerase/dna
source organism Deinococcus radiodurans
molecule keywords Putative Type I topoisomerase
total genus 109
structure length 304
sequence length 337
ec nomenclature
pdb deposition date 2010-03-10

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01028 Topoisom_I Eukaryotic DNA topoisomerase I, catalytic core
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.132.120 Mainly Alpha Orthogonal Bundle Topoisomerase I; Chain A, domain 4 Topoisomerase I; Chain A, domain 4 3m4aA02
3.30.66.10 Alpha Beta 2-Layer Sandwich Viral Topoisomerase I DNA topoisomerase I domain 3m4aA01
3.90.15.10 Alpha Beta Alpha-Beta Complex Topoisomerase I; Chain A, domain 3 Topoisomerase I; Chain A, domain 3 3m4aA03
1SC7A 1NH3A 1LPQA 1TL8A 1A31A 1VCCA 1A35A 2H7GX 1RRJA 1K4SA 1RR8C 1K4TA 1EJ9A 1T8IA 1R49A 1SEUA 2H7FX 2B9SA 1A36A 2F4QA 3IGCA 3M4AA 1A41A
chains in the Genus database with same CATH superfamily
1SC7A 2E2IA 1V9MA 4FXDA 3CQZA 5CQGA 5MLC9 2A69D 1YNJD 2R93A 2YU9A 2CW0D 3GTGA 1R5ZA 3GTKA 2WB1A 4F3EA 3GTOA 1K4SA 2O5JD 4D3YA 3LHPS 1R9TA 2NVYA 3IAYA 2R7ZA 4KDDA 1I50A 3GTPA 3DU5A 1SFOA 4LMOA 4AHCA 2BE5D 1WQGA 4EJ3A 2A6HD 4AN8A 2VUMA 2A68D 1I3QA 1DD5A 4IP9A 4JLRC 1MIUA 1GE9A 3SJRA 4KC6A 2JA5A 3GTQA 1EJ9A 1ISEA 1T8IA 1R49A 3DU6A 1Y1VA 3K58A 1EK8A 2R4GA 1K83A 4KB4A 4AYBA 1TWFA 3IGCA 3K5NA 4Q5GA 3GTJA 1TGOA 2WAQA 1IS1A 3LF9A 1TWGA 1NH3A 2R92A 1VCCA 1TWAA 1A35A 2PMZA 5JSNB 2B9SB 4D3ZA 1RRJA 2H7GX 3GTLA 4IP8A 4L8IA 1K4TA 3MAQA 4OYDB 4GFQA 2JA7A 4QCLA 1SEUA 1TWHA 2H7FX 2B9SA 3KYLA 3GTMA 3WVOA 1A36A 2F4QA 1Y1WA 2B63A 1EH1A 3K5OA 4NOKA 4H3TA 1ZYRD 1SMYD 1IW7D 2NVXA 1WQFA 1Q8IA 1I6VD 1WQHA 4FGUA 1LPQA 1TWCA 1TL8A 1A31A 2JA6A 3K57A 4O26A 5JSBB 1Y698 4QIWA 5C9HA 4NOLA 3K5LA 1RR8C 4FYDA 4C2MA 4KB2A 3K59A 2A6ED 2Y0SA 3H0GA 3K5MA 2E2HA 3FKIA 4KAWX 3M4AA 1WCMA 1HQMD 4Q5VA 4NOMA 3HKZA 1A41A 3P9AA 1YNND
chains in the Genus database with same CATH topology
1SC7A 2E2IA 1V9MA 4FXDA 3CQZA 5CQGA 5MLC9 2A69D 1YNJD 2R93A 2YU9A 2CW0D 3GTGA 1R5ZA 3GTKA 2WB1A 4F3EA 3GTOA 1K4SA 2O5JD 4D3YA 3LHPS 1R9TA 2NVYA 3IAYA 2R7ZA 4KDDA 1I50A 3GTPA 3DU5A 1SFOA 4LMOA 4AHCA 2BE5D 1WQGA 4EJ3A 2A6HD 4AN8A 2VUMA 2A68D 1I3QA 1DD5A 4IP9A 4JLRC 1MIUA 1GE9A 3SJRA 4KC6A 2JA5A 3GTQA 1EJ9A 1ISEA 1T8IA 1R49A 3DU6A 1Y1VA 3K58A 1EK8A 2R4GA 1K83A 4KB4A 4AYBA 1TWFA 3IGCA 3K5NA 4Q5GA 3GTJA 1TGOA 2WAQA 1IS1A 3LF9A 1TWGA 1NH3A 2R92A 1VCCA 1TWAA 1A35A 2PMZA 5JSNB 2B9SB 4D3ZA 1RRJA 2H7GX 3GTLA 4IP8A 4L8IA 1K4TA 3MAQA 4OYDB 4GFQA 2JA7A 4QCLA 1SEUA 1TWHA 2H7FX 2B9SA 3KYLA 3GTMA 3WVOA 1A36A 2F4QA 1Y1WA 2B63A 1EH1A 3K5OA 4NOKA 4H3TA 1ZYRD 1SMYD 1IW7D 2NVXA 1WQFA 1Q8IA 1I6VD 1WQHA 4FGUA 1LPQA 1TWCA 1TL8A 1A31A 2JA6A 3K57A 4O26A 5JSBB 1Y698 4QIWA 5C9HA 4NOLA 3K5LA 1RR8C 4FYDA 4C2MA 4KB2A 3K59A 2A6ED 2Y0SA 3H0GA 3K5MA 2E2HA 3FKIA 4KAWX 3M4AA 1WCMA 1HQMD 4Q5VA 4NOMA 3HKZA 1A41A 3P9AA 1YNND
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1SC7 A;  1NH3 A;  1LPQ A;  1TL8 A;  1A31 A;  1VCC A;  1A35 A;  2H7G X;  1RRJ A;  1K4S A;  1RR8 C;  1K4T A;  1EJ9 A;  1T8I A;  1R49 A;  1SEU A;  2H7F X;  2B9S A;  1A36 A;  2F4Q A;  3IGC A;  3M4A A;  1A41 A; 
#chains in the Genus database with same CATH topology
 1SC7 A;  2E2I A;  1V9M A;  4FXD A;  3CQZ A;  5CQG A;  5MLC 9;  2A69 D;  1YNJ D;  2R93 A;  2YU9 A;  2CW0 D;  3GTG A;  1R5Z A;  3GTK A;  2WB1 A;  4F3E A;  3GTO A;  1K4S A;  2O5J D;  4D3Y A;  3LHP S;  1R9T A;  2NVY A;  3IAY A;  2R7Z A;  4KDD A;  1I50 A;  3GTP A;  3DU5 A;  1SFO A;  4LMO A;  4AHC A;  2BE5 D;  1WQG A;  4EJ3 A;  2A6H D;  4AN8 A;  2VUM A;  2A68 D;  1I3Q A;  1DD5 A;  4IP9 A;  4JLR C;  1MIU A;  1GE9 A;  3SJR A;  4KC6 A;  2JA5 A;  3GTQ A;  1EJ9 A;  1ISE A;  1T8I A;  1R49 A;  3DU6 A;  1Y1V A;  3K58 A;  1EK8 A;  2R4G A;  1K83 A;  4KB4 A;  4AYB A;  1TWF A;  3IGC A;  3K5N A;  4Q5G A;  3GTJ A;  1TGO A;  2WAQ A;  1IS1 A;  3LF9 A;  1TWG A;  1NH3 A;  2R92 A;  1VCC A;  1TWA A;  1A35 A;  2PMZ A;  5JSN B;  2B9S B;  4D3Z A;  1RRJ A;  2H7G X;  3GTL A;  4IP8 A;  4L8I A;  1K4T A;  3MAQ A;  4OYD B;  4GFQ A;  2JA7 A;  4QCL A;  1SEU A;  1TWH A;  2H7F X;  2B9S A;  3KYL A;  3GTM A;  3WVO A;  1A36 A;  2F4Q A;  1Y1W A;  2B63 A;  1EH1 A;  3K5O A;  4NOK A;  4H3T A;  1ZYR D;  1SMY D;  1IW7 D;  2NVX A;  1WQF A;  1Q8I A;  1I6V D;  1WQH A;  4FGU A;  1LPQ A;  1TWC A;  1TL8 A;  1A31 A;  2JA6 A;  3K57 A;  4O26 A;  5JSB B;  1Y69 8;  4QIW A;  5C9H A;  4NOL A;  3K5L A;  1RR8 C;  4FYD A;  4C2M A;  4KB2 A;  3K59 A;  2A6E D;  2Y0S A;  3H0G A;  3K5M A;  2E2H A;  3FKI A;  4KAW X;  3M4A A;  1WCM A;  1HQM D;  4Q5V A;  4NOM A;  3HKZ A;  1A41 A;  3P9A A;  1YNN D; 
#chains in the Genus database with same CATH homology
 1SC7 A;  2E2I A;  1V9M A;  4FXD A;  3CQZ A;  5CQG A;  5MLC 9;  2A69 D;  1YNJ D;  2R93 A;  2YU9 A;  2CW0 D;  3GTG A;  1R5Z A;  3GTK A;  2WB1 A;  4F3E A;  3GTO A;  1K4S A;  2O5J D;  4D3Y A;  3LHP S;  1R9T A;  2NVY A;  3IAY A;  2R7Z A;  4KDD A;  1I50 A;  3GTP A;  3DU5 A;  1SFO A;  4LMO A;  4AHC A;  2BE5 D;  1WQG A;  4EJ3 A;  2A6H D;  4AN8 A;  2VUM A;  2A68 D;  1I3Q A;  1DD5 A;  4IP9 A;  4JLR C;  1MIU A;  1GE9 A;  3SJR A;  4KC6 A;  2JA5 A;  3GTQ A;  1EJ9 A;  1ISE A;  1T8I A;  1R49 A;  3DU6 A;  1Y1V A;  3K58 A;  1EK8 A;  2R4G A;  1K83 A;  4KB4 A;  4AYB A;  1TWF A;  3IGC A;  3K5N A;  4Q5G A;  3GTJ A;  1TGO A;  2WAQ A;  1IS1 A;  3LF9 A;  1TWG A;  1NH3 A;  2R92 A;  1VCC A;  1TWA A;  1A35 A;  2PMZ A;  5JSN B;  2B9S B;  4D3Z A;  1RRJ A;  2H7G X;  3GTL A;  4IP8 A;  4L8I A;  1K4T A;  3MAQ A;  4OYD B;  4GFQ A;  2JA7 A;  4QCL A;  1SEU A;  1TWH A;  2H7F X;  2B9S A;  3KYL A;  3GTM A;  3WVO A;  1A36 A;  2F4Q A;  1Y1W A;  2B63 A;  1EH1 A;  3K5O A;  4NOK A;  4H3T A;  1ZYR D;  1SMY D;  1IW7 D;  2NVX A;  1WQF A;  1Q8I A;  1I6V D;  1WQH A;  4FGU A;  1LPQ A;  1TWC A;  1TL8 A;  1A31 A;  2JA6 A;  3K57 A;  4O26 A;  5JSB B;  1Y69 8;  4QIW A;  5C9H A;  4NOL A;  3K5L A;  1RR8 C;  4FYD A;  4C2M A;  4KB2 A;  3K59 A;  2A6E D;  2Y0S A;  3H0G A;  3K5M A;  2E2H A;  3FKI A;  4KAW X;  3M4A A;  1WCM A;  1HQM D;  4Q5V A;  4NOM A;  3HKZ A;  1A41 A;  3P9A A;  1YNN D; 
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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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