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
source organism Deinococcus radiodurans
molecule tags Isomerase/dna
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
2H7GX 3IGCA 2B9SA 1RRJA 1RR8C 1TL8A 1EJ9A 1VCCA 2H7FX 2F4QA 1SEUA 1A31A 1A41A 1K4TA 1A36A 1T8IA 1SC7A 1NH3A 1K4SA 1LPQA 3M4AA 1A35A 1R49A
chains in the Genus database with same CATH superfamily
2A6HD 3K57A 2NVYA 3K5OA 1WCMA 2VUMA 2A69D 4QIWA 1RR8C 3GTQA 3P9AA 1EJ9A 3SJRA 2BE5D 1HQMD 1GE9A 1SEUA 2NVXA 3MAQA 1WQHA 3K59A 1K4TA 1A36A 4L8IA 4JLRC 1SFOA 4QCLA 3KYLA 1IS1A 4KB2A 3DU6A 2JA7A 4FYDA 2R93A 4H3TA 1R49A 1Y1WA 2H7GX 1WQFA 3DU5A 1TWFA 1K83A 1V9MA 3FKIA 4KC6A 2H7FX 4AN8A 1ISEA 1I50A 2R7ZA 4NOLA 1TWHA 1I3QA 3HKZA 1EK8A 4D3YA 3GTPA 2E2IA 5CQGA 3K5LA 4IP9A 2JA6A 4IP8A 4AHCA 5JSBB 1TGOA 3K5NA 3GTKA 2E2HA 1SC7A 2Y0SA 5C9HA 1K4SA 1A35A 3GTOA 2R4GA 4KB4A 4OYDB 3IGCA 2A6ED 4C2MA 2CW0D 1SMYD 2B9SA 2B9SB 1Y698 3GTGA 1EH1A 4NOMA 4KDDA 1R9TA 1VCCA 2R92A 2F4QA 1ZYRD 4AYBA 3LF9A 3IAYA 1TWGA 1MIUA 2PMZA 5MLC9 1TWAA 3WVOA 4F3EA 1T8IA 1TWCA 4D3ZA 1IW7D 4FGUA 1YNND 5JSNB 1LPQA 1TL8A 4O26A 3LHPS 1YNJD 2A68D 1DD5A 3GTJA 1Q8IA 2WAQA 1R5ZA 1RRJA 4FXDA 2B63A 3GTMA 4LMOA 4KAWX 4GFQA 1A31A 3H0GA 4Q5VA 3K58A 2O5JD 1A41A 3GTLA 2WB1A 3K5MA 1Y1VA 4Q5GA 1WQGA 3CQZA 2YU9A 1NH3A 2JA5A 1I6VD 3M4AA 4NOKA 4EJ3A
chains in the Genus database with same CATH topology
2A6HD 3K57A 2NVYA 3K5OA 1WCMA 2VUMA 2A69D 4QIWA 1RR8C 3GTQA 3P9AA 1EJ9A 3SJRA 2BE5D 1HQMD 1GE9A 1SEUA 2NVXA 3MAQA 1WQHA 3K59A 1K4TA 1A36A 4L8IA 4JLRC 1SFOA 4QCLA 3KYLA 1IS1A 4KB2A 3DU6A 2JA7A 4FYDA 2R93A 4H3TA 1R49A 1Y1WA 2H7GX 1WQFA 3DU5A 1TWFA 1K83A 1V9MA 3FKIA 4KC6A 2H7FX 4AN8A 1ISEA 1I50A 2R7ZA 4NOLA 1TWHA 1I3QA 3HKZA 1EK8A 4D3YA 3GTPA 2E2IA 5CQGA 3K5LA 4IP9A 2JA6A 4IP8A 4AHCA 5JSBB 1TGOA 3K5NA 3GTKA 2E2HA 1SC7A 2Y0SA 5C9HA 1K4SA 1A35A 3GTOA 2R4GA 4KB4A 4OYDB 3IGCA 2A6ED 4C2MA 2CW0D 1SMYD 2B9SA 2B9SB 1Y698 3GTGA 1EH1A 4NOMA 4KDDA 1R9TA 1VCCA 2R92A 2F4QA 1ZYRD 4AYBA 3LF9A 3IAYA 1TWGA 1MIUA 2PMZA 5MLC9 1TWAA 3WVOA 4F3EA 1T8IA 1TWCA 4D3ZA 1IW7D 4FGUA 1YNND 5JSNB 1LPQA 1TL8A 4O26A 3LHPS 1YNJD 2A68D 1DD5A 3GTJA 1Q8IA 2WAQA 1R5ZA 1RRJA 4FXDA 2B63A 3GTMA 4LMOA 4KAWX 4GFQA 1A31A 3H0GA 4Q5VA 3K58A 2O5JD 1A41A 3GTLA 2WB1A 3K5MA 1Y1VA 4Q5GA 1WQGA 3CQZA 2YU9A 1NH3A 2JA5A 1I6VD 3M4AA 4NOKA 4EJ3A
chains in the Genus database with same CATH homology


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