3VMK | Genus

Total Genus 127

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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	127
sequence length	369
structure length	369
Chain Sequence	HHHHHGSSYQIAVLAGDGIGPEVMAEARKVLAAVEKRFDLSIEYSEYDVGGAAIDNHGCPLPEATLKGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSPLRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFESAQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDVMLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQILSAALLLRHSLKLEDAALAIEAAVSKALSDGYLTCELLPASERSQAKSTSQMGDYIAQAIAEG

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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

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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

publication title	Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1 pubmed doi rcsb
molecule keywords	3-isopropylmalate dehydrogenase
molecule tags	Oxidoreductase
source organism	Shewanella benthica
total genus	127
structure length	369
sequence length	369
chains with identical sequence	B
ec nomenclature	ec 1.1.1.85: 3-isopropylmalate dehydrogenase.
pdb deposition date	2011-12-13

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	3vmkA00

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations