5D1CA

Crystal structure of d233g-y306f hdac8 in complex with a tetrapeptide substrate
Total Genus 134
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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
134
sequence length
364
structure length
364
Chain Sequence
LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQGGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV
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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 Hydrolase
molecule keywords Histone deacetylase 8
publication title Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia de Lange Syndrome Spectrum Disorders.
pubmed doi rcsb
source organism Homo sapiens
total genus 134
structure length 364
sequence length 364
chains with identical sequence B
ec nomenclature ec 3.5.1.98: Histone deacetylase.
pdb deposition date 2015-08-04

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
ClassArchitectureTopologyHomologyDomain
3.40.800.20 Alpha Beta 3-Layer(aba) Sandwich Arginase; Chain A Histone deacetylase domain 5d1cA00
1C3PA 2VQWG 5JI5A 3F07A 5G0YA 5FUEA 4QA3A 3Q9CA 5DC6A 4ZUOA 5G17A 5EF7A 4ZUNA 1C3SA 5DC7A 5EEFA 3C10A 5D1CA 1ZZ1A 5G11A 4BZ9A 4QA0A 4RN2A 5EFNA 5G12A 4RN1A 5G0XA 2VCGA 5EENA 3Q9EA 4CQFA 1T67A 3SFHA 5A2SA 2VQMA 4LY1A 1T64A 5G10A 5IX0A 3MZ4A 3MAXA 4ZUMA 5EFHA 5DC8A 2V5WA 5EFJD 3SFFA 3F06A 3EZPA 2VQQA 2VQVA 5THVA 5DC5A 4QA1A 4ZUQA 3MENA 5G1BA 5G0IA 2V5XA 1W22A 1ZZ0A 5IWGA 5EEMA 3EZTA 5FCWA 5D1DA 4ZUPA 1ZZ3A 4RN0A 3MZ6A 4CBYA 5EEIA 5EFBD 5G1CA 4CBTA 2VQOA 3EW8A 5G0GA 5THUA 3ZNSA 1VKGA 1C3RA 4BZ8A 3EWFA 4LXZA 5G0JA 5ICNB 3RQDA 5G3WA 5EFGA 4QA6A 5G0HA 4BZ7A 3ZNRA 5BWZA 4QA7A 2GH6A 3C0YA 5G1AA 5THTA 4QA5A 4QA4A 5D1BA 4ZURA 4BZ6A 3MZ3A 5EEKA 4BKXB 5EF8A 3F0RA 4A69A 1T69A 4BZ5A 3Q9BA 3MZ7A 3C0ZA 5THSA 2VQJA 5LI3A 3Q9FA 5G13A 4QA2A 5EFKB
chains in the Genus database with same CATH superfamily
3GMZA 3SJTA 4IXUA 4MXRA 1C3PA 2VQWG 1WOGA 5JI5A 3F07A 5G0YA 4RHIA 5FUEA 4QA3A 3SL0A 3Q9CA 5DC6A 1XFKA 3CEVA 1WOHA 3NIQA 2PLLA 3LP4A 4Q3RA 3MFWA 4ZUOA 1T4RA 4CEVA 1T4SA 5G17A 4IU4A 5EF7A 4HZEA 4ZUNA 1C3SA 5DC7A 1CEVA 5EEFA 3C10A 4IE3A 3MFVA 5D1CA 1ZZ1A 4Q3PA 5G11A 4GWDA 4FCKA 1P8QA 5HJ9A 4BZ9A 1WOIA 4RHQA 4Q3SA 4QA0A 1P8PA 1HQXA 4RN2A 3F80A 1HQGA 4RHLA 5EFNA 1TBHA 5G12A 1P8OA 4Q3VA 3LP7A 3SL1A 4RN1A 5G0XA 1WVBA 1TBJA 2VCGA 3M1RA 5EENA 1P8MA 3Q9EA 4CQFA 1T67A 4RLAA 4IE2A 3SFHA 2EF5A 5A2SA 2VQMA 3DJ8A 1T5GA 4LY1A 1T64A 1WVAA 5G10A 5IX0A 4GSMA 4FCIA 3MZ4A 3LHLA 3MAXA 3MMRA 4ZUMA 3E6VA 5EFHA 1P8NA 5DC8A 2V5WA 5EFJD 3SFFA 3F06A 3EZPA 2VQQA 2VQVA 5THVA 5DC5A 2EIVA 4RHJA 4I06A 3E9BA 4QA1A 2ZAVA 4ZUQA 3MENA 2A0MA 4Q3UA 5G1BA 2PHOA 1D3VA 5G0IA 2V5XA 1P8SA 1W22A 3THEA 1ZZ0A 4Q3RC 5IWGA 4Q3TA 5EEMA 3EZTA 5FCWA 1GQ7A 4RHMA 5HJAA 4IU5A 5D1DA 1PQ3A 1TBLA 1T4PA 1ZZ3A 4RN0A 3MZ6A 4ZUPA 1P8RA 4CBYA 4MYNA 5EEIA 5EFBD 4DZ4A 1GQ6A 5G1CA 4HWWA 4CBTA 2VQOA 3EW8A 5G0GA 2CEVA 1ZPGA 4GWCA 5THUA 3ZNSA 4Q3QA 1VKGA 5CEVA 1C3RA 4BZ8A 3RLAA 3EWFA 4LXZA 3TF3A 5RLAA 5G0JA 3THHA 5ICNB 3RQDA 5G3WA 5EFGA 4QA6A 4G3HA 4IU0A 5G0HA 3SKKA 3ZNRA 4BZ7A 4Q40A 4ITYA 2PHAA 5BWZA 4IE1A 3TH7A 3NIOA 1T4TA 4QA7A 4Q41A 3MJLA 2AEBA 2GH6A 4IU1A 3C0YA 1RLAA 1HQFA 2RLAA 3E6KA 4IXVA 1HQ5A 3GN0A 4RHKA 4MYKA 4QA5A 5G1AA 5THTA 4QA4A 5D1BA 4ZURA 1TA1A 4BZ6A 3MZ3A 5EEKA 4BKXB 3NIPA 4MYFA 3KV2A 5EF8A 1HQHA 1T5FA 2EF4A 3F0RA 4A69A 4HXQA 1T69A 3PZLA 4BZ5A 3E8ZA 1ZPEA 3Q9BA 3MZ7A 3C0ZA 4GSVA 4Q42A 5THSA 4GSZA 3E8QA 2VQJA 1R1OA 4MYLA 5LI3A 3Q9FA 5G13A 3THJA 4QA2A 5EFKB
chains in the Genus database with same CATH topology
1C3PA 2VQWG 5JI5A 3F07A 5G0YA 5FUEA 4QA3A 3Q9CA 5DC6A 4ZUOA 5G17A 5EF7A 4ZUNA 1C3SA 5DC7A 5EEFA 3C10A 5D1CA 1ZZ1A 5G11A 4BZ9A 4QA0A 4RN2A 5EFNA 5G12A 4RN1A 5G0XA 2VCGA 5EENA 3Q9EA 4CQFA 1T67A 3SFHA 5A2SA 2VQMA 4LY1A 1T64A 5G10A 5IX0A 3MZ4A 3MAXA 4ZUMA 5EFHA 5DC8A 2V5WA 5EFJD 3SFFA 3F06A 3EZPA 2VQQA 2VQVA 5THVA 5DC5A 4QA1A 4ZUQA 3MENA 5G1BA 5G0IA 2V5XA 1W22A 1ZZ0A 5IWGA 5EEMA 3EZTA 5FCWA 5D1DA 4ZUPA 1ZZ3A 4RN0A 3MZ6A 4CBYA 5EEIA 5EFBD 5G1CA 4CBTA 2VQOA 3EW8A 5G0GA 5THUA 3ZNSA 1VKGA 1C3RA 4BZ8A 3EWFA 4LXZA 5G0JA 5ICNB 3RQDA 5G3WA 5EFGA 4QA6A 5G0HA 4BZ7A 3ZNRA 5BWZA 4QA7A 2GH6A 3C0YA 5G1AA 5THTA 4QA5A 4QA4A 5D1BA 4ZURA 4BZ6A 3MZ3A 5EEKA 4BKXB 5EF8A 3F0RA 4A69A 1T69A 4BZ5A 3Q9BA 3MZ7A 3C0ZA 5THSA 2VQJA 5LI3A 3Q9FA 5G13A 4QA2A 5EFKB
chains in the Genus database with same CATH homology


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