3M4AA

Crystal structure of a bacterial topoisomerase ib in complex with dna reveals a secondary dna binding site
Total Genus 109
Loading diagram...

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
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...