5EEM | Genus

Total Genus 136

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	136
sequence length	356
structure length	354
Chain Sequence	PITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDTPLKTSATVSINNVLRAHAPFWSSL

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/5d0103cb84c06aa91cdad840/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d0103cb84c06aa91cdad840/pdb.gz): 1004 ms

reading 354 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

354 atoms created

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

Time for creating model: 26 ms

Adding embedded #jmolscript: select ({0:353});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

molecule tags	Hydrolase
source organism	Danio rerio
publication title	Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. pubmed doi rcsb
molecule keywords	Hdac6 protein
total genus	136
structure length	354
sequence length	356
chains with identical sequence	B
ec nomenclature	ec 3.5.1.98: Histone deacetylase.
pdb deposition date	2015-10-23

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00850	Hist_deacetyl	Histone deacetylase domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase; Chain A	Histone deacetylase domain	5eemA00

5G0IA 5D1DA 2VCGA 4LXZA 4RN1A 5THVA 4ZUNA 4QA5A 4QA7A 3MZ6A 5G0GA 5G0JA 5G3WA 4A69A 4RN2A 5G0HA 5FUEA 4ZURA 3EZPA 3C0ZA 5EFKB 3EW8A 3Q9FA 5EF7A 4BKXB 5D1CA 1ZZ0A 4QA2A 4BZ7A 5EFNA 3C10A 1VKGA 5EEKA 1T67A 5DC6A 5EFGA 5G0YA 5G12A 5EEMA 3Q9CA 5ICNB 2GH6A 3SFFA 5EEFA 5DC7A 5FCWA 3F0RA 3EZTA 5G1CA 5G11A 3MAXA 5G1BA 5A2SA 5LI3A 1C3RA 3Q9BA 5EFJD 2VQMA 5THTA 1W22A 5EEIA 3Q9EA 5DC8A 5G1AA 5G10A 5DC5A 4CQFA 1C3PA 5EENA 4BZ9A 4QA4A 4QA1A 2VQQA 5EFHA 5G13A 5JI5A 2VQOA 2VQJA 1ZZ1A 3SFHA 1C3SA 5G17A 4BZ8A 2VQVA 3F07A 3F06A 5THUA 4QA3A 2V5XA 4BZ5A 4RN0A 1T64A 4QA6A 4CBTA 5EF8A 3MENA 4CBYA 3C0YA 5EFBD 5IWGA 2V5WA 1T69A 5THSA 3ZNSA 4ZUQA 4ZUMA 3MZ4A 4QA0A 2VQWG 5BWZA 4BZ6A 4LY1A 3MZ7A 5IX0A 3ZNRA 5D1BA 3MZ3A 4ZUPA 4ZUOA 1ZZ3A 5G0XA 3RQDA 3EWFA
chains in the Genus database with same CATH superfamily

1R1OA 1HQXA 5G0IA 5D1DA 1PQ3A 2VCGA 3TF3A 1TBHA 4LXZA 4Q3RA 4RN1A 3LHLA 5THVA 3GN0A 3THHA 1T4SA 4ZUNA 1XFKA 4QA5A 4QA7A 3MZ6A 5G0GA 5G0JA 5G3WA 4A69A 1WOGA 3E8ZA 4RN2A 1HQFA 1T4TA 5FUEA 5G0HA 4ZURA 3EZPA 4CEVA 3C0ZA 5EFKB 3EW8A 3Q9FA 5EF7A 2EF5A 4BKXB 1T4RA 4RHQA 5D1CA 1ZZ0A 4QA2A 4BZ7A 4RHMA 5EFNA 3E6VA 5CEVA 3C10A 4Q3TA 4GSVA 2PHOA 4IE2A 1WOIA 1VKGA 5EEKA 1T67A 3TH7A 5DC6A 4IU1A 5EFGA 5G0YA 4MYLA 4MYKA 5G12A 5EEMA 3Q9CA 5ICNB 3SKKA 2ZAVA 4FCKA 3E8QA 2GH6A 3SFFA 5EEFA 1CEVA 5DC7A 5FCWA 3F0RA 3M1RA 4RHJA 3EZTA 5G1CA 4IXVA 1GQ7A 1P8PA 5HJAA 4Q42A 4Q3UA 4RHLA 5G11A 1GQ6A 3MAXA 5G1BA 5A2SA 5LI3A 1C3RA 3Q9BA 4RHIA 5EFJD 2VQMA 1TBJA 4MYFA 1W22A 5EEIA 5THTA 3MFVA 3Q9EA 5DC8A 2CEVA 4GSMA 5RLAA 3MJLA 4GWCA 5G1AA 5G10A 5DC5A 1P8MA 4CQFA 2EF4A 1C3PA 4MXRA 5EENA 4BZ9A 1HQ5A 1TBLA 1TA1A 3DJ8A 3MMRA 4Q41A 3E9BA 3NIOA 4QA4A 4Q3VA 1T5FA 4Q40A 4QA1A 2VQQA 4HXQA 3SJTA 4I06A 1WOHA 5EFHA 3SL1A 4G3HA 2PHAA 3MFWA 4IXUA 4GWDA 3LP7A 5G13A 5JI5A 2A0MA 1P8OA 2VQOA 2VQJA 1ZZ1A 4Q3RC 3SFHA 1C3SA 1WVBA 4FCIA 3SL0A 1ZPEA 1T5GA 4IU0A 1HQHA 5G17A 3THJA 2VQVA 1ZPGA 3F07A 3F06A 5THUA 4BZ8A 4IE3A 2V5XA 1P8RA 3CEVA 4QA3A 4BZ5A 4RN0A 1T64A 4QA6A 4RHKA 3F80A 3KV2A 2RLAA 1P8QA 3PZLA 4CBTA 4MYNA 2EIVA 2PLLA 4HZEA 5EF8A 3MENA 4CBYA 3C0YA 5EFBD 5IWGA 4IU5A 4IU4A 2V5WA 1P8NA 1T69A 5THSA 4GSZA 3ZNSA 4HWWA 4ZUMA 5HJ9A 4ZUQA 3GMZA 3THEA 3MZ4A 3NIQA 4Q3QA 4QA0A 3LP4A 1RLAA 1P8SA 2VQWG 4RLAA 5BWZA 1T4PA 4ITYA 1HQGA 4LY1A 4BZ6A 4Q3SA 3MZ7A 3E6KA 2AEBA 5IX0A 3NIPA 5D1BA 3ZNRA 3MZ3A 3RLAA 4ZUPA 4DZ4A 1D3VA 4Q3PA 4ZUOA 1WVAA 4IE1A 1ZZ3A 5G0XA 3RQDA 3EWFA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 5G0I A;  5D1D A;  2VCG A;  4LXZ A;  4RN1 A;  5THV A;  4ZUN A;  4QA5 A;  4QA7 A;  3MZ6 A;  5G0G A;  5G0J A;  5G3W A;  4A69 A;  4RN2 A;  5G0H A;  5FUE A;  4ZUR A;  3EZP A;  3C0Z A;  5EFK B;  3EW8 A;  3Q9F A;  5EF7 A;  4BKX B;  5D1C A;  1ZZ0 A;  4QA2 A;  4BZ7 A;  5EFN A;  3C10 A;  1VKG A;  5EEK A;  1T67 A;  5DC6 A;  5EFG A;  5G0Y A;  5G12 A;  5EEM A;  3Q9C A;  5ICN B;  2GH6 A;  3SFF A;  5EEF A;  5DC7 A;  5FCW A;  3F0R A;  3EZT A;  5G1C A;  5G11 A;  3MAX A;  5G1B A;  5A2S A;  5LI3 A;  1C3R A;  3Q9B A;  5EFJ D;  2VQM A;  5THT A;  1W22 A;  5EEI A;  3Q9E A;  5DC8 A;  5G1A A;  5G10 A;  5DC5 A;  4CQF A;  1C3P A;  5EEN A;  4BZ9 A;  4QA4 A;  4QA1 A;  2VQQ A;  5EFH A;  5G13 A;  5JI5 A;  2VQO A;  2VQJ A;  1ZZ1 A;  3SFH A;  1C3S A;  5G17 A;  4BZ8 A;  2VQV A;  3F07 A;  3F06 A;  5THU A;  4QA3 A;  2V5X A;  4BZ5 A;  4RN0 A;  1T64 A;  4QA6 A;  4CBT A;  5EF8 A;  3MEN A;  4CBY A;  3C0Y A;  5EFB D;  5IWG A;  2V5W A;  1T69 A;  5THS A;  3ZNS A;  4ZUQ A;  4ZUM A;  3MZ4 A;  4QA0 A;  2VQW G;  5BWZ A;  4BZ6 A;  4LY1 A;  3MZ7 A;  5IX0 A;  3ZNR A;  5D1B A;  3MZ3 A;  4ZUP A;  4ZUO A;  1ZZ3 A;  5G0X A;  3RQD A;  3EWF A; 
#chains in the Genus database with same CATH topology
 1R1O A;  1HQX A;  5G0I A;  5D1D A;  1PQ3 A;  2VCG A;  3TF3 A;  1TBH A;  4LXZ A;  4Q3R A;  4RN1 A;  3LHL A;  5THV A;  3GN0 A;  3THH A;  1T4S A;  4ZUN A;  1XFK A;  4QA5 A;  4QA7 A;  3MZ6 A;  5G0G A;  5G0J A;  5G3W A;  4A69 A;  1WOG A;  3E8Z A;  4RN2 A;  1HQF A;  1T4T A;  5FUE A;  5G0H A;  4ZUR A;  3EZP A;  4CEV A;  3C0Z A;  5EFK B;  3EW8 A;  3Q9F A;  5EF7 A;  2EF5 A;  4BKX B;  1T4R A;  4RHQ A;  5D1C A;  1ZZ0 A;  4QA2 A;  4BZ7 A;  4RHM A;  5EFN A;  3E6V A;  5CEV A;  3C10 A;  4Q3T A;  4GSV A;  2PHO A;  4IE2 A;  1WOI A;  1VKG A;  5EEK A;  1T67 A;  3TH7 A;  5DC6 A;  4IU1 A;  5EFG A;  5G0Y A;  4MYL A;  4MYK A;  5G12 A;  5EEM A;  3Q9C A;  5ICN B;  3SKK A;  2ZAV A;  4FCK A;  3E8Q A;  2GH6 A;  3SFF A;  5EEF A;  1CEV A;  5DC7 A;  5FCW A;  3F0R A;  3M1R A;  4RHJ A;  3EZT A;  5G1C A;  4IXV A;  1GQ7 A;  1P8P A;  5HJA A;  4Q42 A;  4Q3U A;  4RHL A;  5G11 A;  1GQ6 A;  3MAX A;  5G1B A;  5A2S A;  5LI3 A;  1C3R A;  3Q9B A;  4RHI A;  5EFJ D;  2VQM A;  1TBJ A;  4MYF A;  1W22 A;  5EEI A;  5THT A;  3MFV A;  3Q9E A;  5DC8 A;  2CEV A;  4GSM A;  5RLA A;  3MJL A;  4GWC A;  5G1A A;  5G10 A;  5DC5 A;  1P8M A;  4CQF A;  2EF4 A;  1C3P A;  4MXR A;  5EEN A;  4BZ9 A;  1HQ5 A;  1TBL A;  1TA1 A;  3DJ8 A;  3MMR A;  4Q41 A;  3E9B A;  3NIO A;  4QA4 A;  4Q3V A;  1T5F A;  4Q40 A;  4QA1 A;  2VQQ A;  4HXQ A;  3SJT A;  4I06 A;  1WOH A;  5EFH A;  3SL1 A;  4G3H A;  2PHA A;  3MFW A;  4IXU A;  4GWD A;  3LP7 A;  5G13 A;  5JI5 A;  2A0M A;  1P8O A;  2VQO A;  2VQJ A;  1ZZ1 A;  4Q3R C;  3SFH A;  1C3S A;  1WVB A;  4FCI A;  3SL0 A;  1ZPE A;  1T5G A;  4IU0 A;  1HQH A;  5G17 A;  3THJ A;  2VQV A;  1ZPG A;  3F07 A;  3F06 A;  5THU A;  4BZ8 A;  4IE3 A;  2V5X A;  1P8R A;  3CEV A;  4QA3 A;  4BZ5 A;  4RN0 A;  1T64 A;  4QA6 A;  4RHK A;  3F80 A;  3KV2 A;  2RLA A;  1P8Q A;  3PZL A;  4CBT A;  4MYN A;  2EIV A;  2PLL A;  4HZE A;  5EF8 A;  3MEN A;  4CBY A;  3C0Y A;  5EFB D;  5IWG A;  4IU5 A;  4IU4 A;  2V5W A;  1P8N A;  1T69 A;  5THS A;  4GSZ A;  3ZNS A;  4HWW A;  4ZUM A;  5HJ9 A;  4ZUQ A;  3GMZ A;  3THE A;  3MZ4 A;  3NIQ A;  4Q3Q A;  4QA0 A;  3LP4 A;  1RLA A;  1P8S A;  2VQW G;  4RLA A;  5BWZ A;  1T4P A;  4ITY A;  1HQG A;  4LY1 A;  4BZ6 A;  4Q3S A;  3MZ7 A;  3E6K A;  2AEB A;  5IX0 A;  3NIP A;  5D1B A;  3ZNR A;  3MZ3 A;  3RLA A;  4ZUP A;  4DZ4 A;  1D3V A;  4Q3P A;  4ZUO A;  1WVA A;  4IE1 A;  1ZZ3 A;  5G0X A;  3RQD A;  3EWF A; 
#chains in the Genus database with same CATH homology
 5G0I A;  5D1D A;  2VCG A;  4LXZ A;  4RN1 A;  5THV A;  4ZUN A;  4QA5 A;  4QA7 A;  3MZ6 A;  5G0G A;  5G0J A;  5G3W A;  4A69 A;  4RN2 A;  5G0H A;  5FUE A;  4ZUR A;  3EZP A;  3C0Z A;  5EFK B;  3EW8 A;  3Q9F A;  5EF7 A;  4BKX B;  5D1C A;  1ZZ0 A;  4QA2 A;  4BZ7 A;  5EFN A;  3C10 A;  1VKG A;  5EEK A;  1T67 A;  5DC6 A;  5EFG A;  5G0Y A;  5G12 A;  5EEM A;  3Q9C A;  5ICN B;  2GH6 A;  3SFF A;  5EEF A;  5DC7 A;  5FCW A;  3F0R A;  3EZT A;  5G1C A;  5G11 A;  3MAX A;  5G1B A;  5A2S A;  5LI3 A;  1C3R A;  3Q9B A;  5EFJ D;  2VQM A;  5THT A;  1W22 A;  5EEI A;  3Q9E A;  5DC8 A;  5G1A A;  5G10 A;  5DC5 A;  4CQF A;  1C3P A;  5EEN A;  4BZ9 A;  4QA4 A;  4QA1 A;  2VQQ A;  5EFH A;  5G13 A;  5JI5 A;  2VQO A;  2VQJ A;  1ZZ1 A;  3SFH A;  1C3S A;  5G17 A;  4BZ8 A;  2VQV A;  3F07 A;  3F06 A;  5THU A;  4QA3 A;  2V5X A;  4BZ5 A;  4RN0 A;  1T64 A;  4QA6 A;  4CBT A;  5EF8 A;  3MEN A;  4CBY A;  3C0Y A;  5EFB D;  5IWG A;  2V5W A;  1T69 A;  5THS A;  3ZNS A;  4ZUQ A;  4ZUM A;  3MZ4 A;  4QA0 A;  2VQW G;  5BWZ A;  4BZ6 A;  4LY1 A;  3MZ7 A;  5IX0 A;  3ZNR A;  5D1B A;  3MZ3 A;  4ZUP A;  4ZUO A;  1ZZ3 A;  5G0X A;  3RQD A;  3EWF 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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#similar chains in the pdb database (?% sequence similarity)
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5EEMA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations