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


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