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


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