2QFY | Genus

Total Genus 142

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	142
sequence length	411
structure length	411
Chain Sequence	FSKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKSI

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

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Viewer cachePut cache://localLOAD_/file/5cfd7f188c360daa5533ba41/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5cfd7f188c360daa5533ba41/pdb.gz): 1760 ms

reading 411 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

411 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 30 ms

Adding embedded #jmolscript: select ({0:410});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Oxidoreductase
source organism	Saccharomyces cerevisiae
publication title	Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction pubmed doi rcsb
molecule keywords	Isocitrate dehydrogenase [NADP]
total genus	142
structure length	411
sequence length	411
chains with identical sequence	B, C, D, E, F
ec nomenclature	ec 1.1.1.42: Isocitrate dehydrogenase (NADP(+)).
pdb deposition date	2007-06-28

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00180	Iso_dh	Isocitrate/isopropylmalate dehydrogenase

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.40.718.10	Alpha Beta	3-Layer(aba) Sandwich	Isopropylmalate Dehydrogenase	Isopropylmalate Dehydrogenase	2qfyA00

4JA8A 3VL6A 5K10A 3VL3A 5L58A 1GC8A 1U7NA 1XABA 1WPWA 3U9EA 1BL5A 3FMXX 1IDMA 1AI3A 4XS3A 3TNGA 5J33A 4JQPA 4AJRA 5GRHA 1PS6A 1XKDA 4UMYA 3ASJA 3BLVA 3WZXA 5GRFA 4L03A 1VLCA 2ZTWA 1GRPA 3LCBC 1TYOA 5I96A 1CW7A 4I3LA 5DE1A 5L57A 5GRLB 1IKAA 1OSJA 4ICDA 1IDFA 1XGVA 5J34A 1XAAA 1IDDA 1YXOA 3MAPA 1HEXA 3UDUA 2E0CA 3AH3A 3ICDA 3US8A 3VMJA 1PTMA 1CW1A 1HQSA 4Y1PA 5I95A 2G4OA 1PB3A 3VMLA 2IV0A 3TSNA 3UDOA 5HN3A 2QFWA 3FLKA 1P8FA 2Y40A 1SJSA 2D1CA 1T09A 1ZORA 2E5MA 1AI2A 4KZOA 4P69C 3TY3A 3VL2A 4AJ3A 1CM7A 4I3KA 1YCOA 3UF6A 4BNPA 4YB4A 2QFVA 1GROA 5GRLA 2QFXA 5HN4A 3VL7A 1V5BA 4AJBA 5GRIB 1IDCA 3VMKA 4XRXA 4AJSA 5LGEA 2UXRA 3U1HA 4UMXA 3MASB 1DPZA 5GREB 5K11A 7ICDA 3WZYA 1T0LA 2DHTA 3BLXB 5HN6A 4AJAA 1XACA 3BLVB 1IPDA 2HI1A 5HN5A 4L06A 1V94A 1DR0A 2AYQA 1PS7A 1WALA 3INMA 4ATYA 3VL4A 2UXQA 1LWDA 1CW4A 3LXYA 1CNZA 2Y42A 3VKZA 9ICDA 6ICDA 1IDEA 1V53A 3WZVA 4IWHA 2Y41A 2QFYA 5GRIA 5ICDA 1GC9A 4XXVA 3TY4A 2D4VA 1DR8A 1G2UA 3R8WA 4AOUA 3MASA 1A05A 1HJ6A 1X0LA 5GREA 3MARA 1W0DA 1R8KA 3WZWA 4WUOA 1PB1A 5GRHB 4AOVA 4AOYA 3BLXA 3DMSA 4AJCA 4F7IA 5J32A 1OSIA 5GRFB 1XADA 1VI1A 2Y3ZA 1ISOA 4HCXA 8ICDA 4L04A
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 4JA8 A;  3VL6 A;  5K10 A;  3VL3 A;  5L58 A;  1GC8 A;  1U7N A;  1XAB A;  1WPW A;  3U9E A;  1BL5 A;  3FMX X;  1IDM A;  1AI3 A;  4XS3 A;  3TNG A;  5J33 A;  4JQP A;  4AJR A;  5GRH A;  1PS6 A;  1XKD A;  4UMY A;  3ASJ A;  3BLV A;  3WZX A;  5GRF A;  4L03 A;  1VLC A;  2ZTW A;  1GRP A;  3LCB C;  1TYO A;  5I96 A;  1CW7 A;  4I3L A;  5DE1 A;  5L57 A;  5GRL B;  1IKA A;  1OSJ A;  4ICD A;  1IDF A;  1XGV A;  5J34 A;  1XAA A;  1IDD A;  1YXO A;  3MAP A;  1HEX A;  3UDU A;  2E0C A;  3AH3 A;  3ICD A;  3US8 A;  3VMJ A;  1PTM A;  1CW1 A;  1HQS A;  4Y1P A;  5I95 A;  2G4O A;  1PB3 A;  3VML A;  2IV0 A;  3TSN A;  3UDO A;  5HN3 A;  2QFW A;  3FLK A;  1P8F A;  2Y40 A;  1SJS A;  2D1C A;  1T09 A;  1ZOR A;  2E5M A;  1AI2 A;  4KZO A;  4P69 C;  3TY3 A;  3VL2 A;  4AJ3 A;  1CM7 A;  4I3K A;  1YCO A;  3UF6 A;  4BNP A;  4YB4 A;  2QFV A;  1GRO A;  5GRL A;  2QFX A;  5HN4 A;  3VL7 A;  1V5B A;  4AJB A;  5GRI B;  1IDC A;  3VMK A;  4XRX A;  4AJS A;  5LGE A;  2UXR A;  3U1H A;  4UMX A;  3MAS B;  1DPZ A;  5GRE B;  5K11 A;  7ICD A;  3WZY A;  1T0L A;  2DHT A;  3BLX B;  5HN6 A;  4AJA A;  1XAC A;  3BLV B;  1IPD A;  2HI1 A;  5HN5 A;  4L06 A;  1V94 A;  1DR0 A;  2AYQ A;  1PS7 A;  1WAL A;  3INM A;  4ATY A;  3VL4 A;  2UXQ A;  1LWD A;  1CW4 A;  3LXY A;  1CNZ A;  2Y42 A;  3VKZ A;  9ICD A;  6ICD A;  1IDE A;  1V53 A;  3WZV A;  4IWH A;  2Y41 A;  2QFY A;  5GRI A;  5ICD A;  1GC9 A;  4XXV A;  3TY4 A;  2D4V A;  1DR8 A;  1G2U A;  3R8W A;  4AOU A;  3MAS A;  1A05 A;  1HJ6 A;  1X0L A;  5GRE A;  3MAR A;  1W0D A;  1R8K A;  3WZW A;  4WUO A;  1PB1 A;  5GRH B;  4AOV A;  4AOY A;  3BLX A;  3DMS A;  4AJC A;  4F7I A;  5J32 A;  1OSI A;  5GRF B;  1XAD A;  1VI1 A;  2Y3Z A;  1ISO A;  4HCX A;  8ICD A;  4L04 A; 
#chains in the Genus database with same CATH topology
 4JA8 A;  3VL6 A;  5K10 A;  3VL3 A;  5L58 A;  1GC8 A;  1U7N A;  1XAB A;  1WPW A;  3U9E A;  1BL5 A;  3FMX X;  1IDM A;  1AI3 A;  4XS3 A;  3TNG A;  5J33 A;  4JQP A;  4AJR A;  5GRH A;  1PS6 A;  1XKD A;  4UMY A;  3ASJ A;  3BLV A;  3WZX A;  5GRF A;  4L03 A;  1VLC A;  2ZTW A;  1GRP A;  3LCB C;  1TYO A;  5I96 A;  1CW7 A;  4I3L A;  5DE1 A;  5L57 A;  5GRL B;  1IKA A;  1OSJ A;  4ICD A;  1IDF A;  1XGV A;  5J34 A;  1XAA A;  1IDD A;  1YXO A;  3MAP A;  1HEX A;  3UDU A;  2E0C A;  3AH3 A;  3ICD A;  3US8 A;  3VMJ A;  1PTM A;  1CW1 A;  1HQS A;  4Y1P A;  5I95 A;  2G4O A;  1PB3 A;  3VML A;  2IV0 A;  3TSN A;  3UDO A;  5HN3 A;  2QFW A;  3FLK A;  1P8F A;  2Y40 A;  1SJS A;  2D1C A;  1T09 A;  1ZOR A;  2E5M A;  1AI2 A;  4KZO A;  4P69 C;  3TY3 A;  3VL2 A;  4AJ3 A;  1CM7 A;  4I3K A;  1YCO A;  3UF6 A;  4BNP A;  4YB4 A;  2QFV A;  1GRO A;  5GRL A;  2QFX A;  5HN4 A;  3VL7 A;  1V5B A;  4AJB A;  5GRI B;  1IDC A;  3VMK A;  4XRX A;  4AJS A;  5LGE A;  2UXR A;  3U1H A;  4UMX A;  3MAS B;  1DPZ A;  5GRE B;  5K11 A;  7ICD A;  3WZY A;  1T0L A;  2DHT A;  3BLX B;  5HN6 A;  4AJA A;  1XAC A;  3BLV B;  1IPD A;  2HI1 A;  5HN5 A;  4L06 A;  1V94 A;  1DR0 A;  2AYQ A;  1PS7 A;  1WAL A;  3INM A;  4ATY A;  3VL4 A;  2UXQ A;  1LWD A;  1CW4 A;  3LXY A;  1CNZ A;  2Y42 A;  3VKZ A;  9ICD A;  6ICD A;  1IDE A;  1V53 A;  3WZV A;  4IWH A;  2Y41 A;  2QFY A;  5GRI A;  5ICD A;  1GC9 A;  4XXV A;  3TY4 A;  2D4V A;  1DR8 A;  1G2U A;  3R8W A;  4AOU A;  3MAS A;  1A05 A;  1HJ6 A;  1X0L A;  5GRE A;  3MAR A;  1W0D A;  1R8K A;  3WZW A;  4WUO A;  1PB1 A;  5GRH B;  4AOV A;  4AOY A;  3BLX A;  3DMS A;  4AJC A;  4F7I A;  5J32 A;  1OSI A;  5GRF B;  1XAD A;  1VI1 A;  2Y3Z A;  1ISO A;  4HCX A;  8ICD A;  4L04 A; 
#chains in the Genus database with same CATH homology
 4JA8 A;  3VL6 A;  5K10 A;  3VL3 A;  5L58 A;  1GC8 A;  1U7N A;  1XAB A;  1WPW A;  3U9E A;  1BL5 A;  3FMX X;  1IDM A;  1AI3 A;  4XS3 A;  3TNG A;  5J33 A;  4JQP A;  4AJR A;  5GRH A;  1PS6 A;  1XKD A;  4UMY A;  3ASJ A;  3BLV A;  3WZX A;  5GRF A;  4L03 A;  1VLC A;  2ZTW A;  1GRP A;  3LCB C;  1TYO A;  5I96 A;  1CW7 A;  4I3L A;  5DE1 A;  5L57 A;  5GRL B;  1IKA A;  1OSJ A;  4ICD A;  1IDF A;  1XGV A;  5J34 A;  1XAA A;  1IDD A;  1YXO A;  3MAP A;  1HEX A;  3UDU A;  2E0C A;  3AH3 A;  3ICD A;  3US8 A;  3VMJ A;  1PTM A;  1CW1 A;  1HQS A;  4Y1P A;  5I95 A;  2G4O A;  1PB3 A;  3VML A;  2IV0 A;  3TSN A;  3UDO A;  5HN3 A;  2QFW A;  3FLK A;  1P8F A;  2Y40 A;  1SJS A;  2D1C A;  1T09 A;  1ZOR A;  2E5M A;  1AI2 A;  4KZO A;  4P69 C;  3TY3 A;  3VL2 A;  4AJ3 A;  1CM7 A;  4I3K A;  1YCO A;  3UF6 A;  4BNP A;  4YB4 A;  2QFV A;  1GRO A;  5GRL A;  2QFX A;  5HN4 A;  3VL7 A;  1V5B A;  4AJB A;  5GRI B;  1IDC A;  3VMK A;  4XRX A;  4AJS A;  5LGE A;  2UXR A;  3U1H A;  4UMX A;  3MAS B;  1DPZ A;  5GRE B;  5K11 A;  7ICD A;  3WZY A;  1T0L A;  2DHT A;  3BLX B;  5HN6 A;  4AJA A;  1XAC A;  3BLV B;  1IPD A;  2HI1 A;  5HN5 A;  4L06 A;  1V94 A;  1DR0 A;  2AYQ A;  1PS7 A;  1WAL A;  3INM A;  4ATY A;  3VL4 A;  2UXQ A;  1LWD A;  1CW4 A;  3LXY A;  1CNZ A;  2Y42 A;  3VKZ A;  9ICD A;  6ICD A;  1IDE A;  1V53 A;  3WZV A;  4IWH A;  2Y41 A;  2QFY A;  5GRI A;  5ICD A;  1GC9 A;  4XXV A;  3TY4 A;  2D4V A;  1DR8 A;  1G2U A;  3R8W A;  4AOU A;  3MAS A;  1A05 A;  1HJ6 A;  1X0L A;  5GRE A;  3MAR A;  1W0D A;  1R8K A;  3WZW A;  4WUO A;  1PB1 A;  5GRH B;  4AOV A;  4AOY A;  3BLX A;  3DMS A;  4AJC A;  4F7I A;  5J32 A;  1OSI A;  5GRF B;  1XAD A;  1VI1 A;  2Y3Z A;  1ISO A;  4HCX A;  8ICD A;  4L04 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)

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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2QFYA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations