4RN0A

Crystal structure of s39d hdac8 in complex with a largazole analogue.
Total Genus 133
50100150200250300350020406080100120140
Genus TraceResidueGenus

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
133
sequence length
365
structure length
359
Chain Sequence
LVPVYIYSPEYVSMCDSLAKIPKRADMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVI
5010015020025030035035030025020015010050
020406080100120Genus Matrix

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
AH4 (73-85)EMPTYAH1 (22-29)TVIII1 (32-35)AH2 (37-48)TI1 (29-32)TII1 (34-37)AH10 (308-323)TIV8 (305-308)TIV2 (99-102)3H1 (50-53)TI6 (145-148)S2 (55-57)S3 (133-136)AH3 (64-68)TIV1 (68-71)TIV4 (129-132)TI2 (98-101)AH5 (107-128)TI4 (136-139)TIV3 (102-105)S8 (298-301)AH8 (237-255)TI5 (141-144)AH6 (157-166)TVIII2 (153-156)O1 (181-183)AH9 (281-294)AH7 (183-189)TI7 (189-192)TVIII3 (169-172)TIV6 (166-169)TVIa1 (207-210)S4 (172-176)S5 (195-202)TIV7 (192-195)TII2 (204-207)S7 (259-263)TI8 (213-216)TII3 (222-225)3H2 (220-222)TI11 (334-337)3H3 (337-339)S6 (226-231)TII4 (232-235)TI10 (272-275)TI9 (266-269)TI12 (341-344)TIV9 (340-343)S1 (17-19)TI3 (101-104)TI'1 (150-153)TII5 (269-272)Updating...
connected with : NaN
molecule tags Hydrolase/hydrolase inhibitor
source organism Homo sapiens
publication title Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8.
pubmed doi rcsb
molecule keywords Histone deacetylase 8
total genus 133
structure length 359
sequence length 365
chains with identical sequence B
ec nomenclature ec 3.5.1.98: Histone deacetylase.
pdb deposition date 2014-10-22

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 4rn0A00
2GH6A 3SFHA 4RN1A 5IWGA 5EF8A 5LI3A 5FUEA 5EF7A 4QA7A 4A69A 4CBTA 4QA4A 5G17A 2V5WA 3F0RA 1C3PA 5G1BA 4BZ8A 2VQOA 2VQJA 3Q9BA 4QA2A 5THSA 5EEIA 1T67A 3EZTA 3RQDA 5EFKB 3F06A 3MAXA 2VQQA 2VQVA 3F07A 4RN0A 5G0XA 4BKXB 5G12A 5G1CA 3MZ3A 4ZUMA 4ZUNA 3EW8A 4ZUPA 3C0YA 4LXZA 1ZZ1A 5DC8A 4BZ7A 3MZ4A 5EEMA 5G0JA 4QA1A 4CQFA 4ZURA 4RN2A 1ZZ0A 5ICNB 5G13A 4BZ6A 5DC5A 3ZNSA 3C10A 1ZZ3A 5EEFA 5D1CA 4ZUOA 4BZ9A 2VQWG 4QA0A 1T69A 3Q9CA 3MZ7A 4QA5A 3C0ZA 2VQMA 5D1BA 5EFGA 5G10A 5FCWA 1C3RA 1W22A 5G11A 1T64A 5G0GA 5IX0A 5THUA 4LY1A 5G1AA 3ZNRA 5EENA 5BWZA 5EFJD 5D1DA 5THTA 3SFFA 4QA3A 3EZPA 3Q9FA 3EWFA 5EFHA 5G0YA 5G3WA 1C3SA 2V5XA 4ZUQA 4BZ5A 1VKGA 2VCGA 4QA6A 5A2SA 5DC6A 3MZ6A 3Q9EA 5G0IA 5JI5A 5EFBD 4CBYA 5G0HA 5EFNA 5EEKA 5DC7A 5THVA 3MENA
chains in the Genus database with same CATH superfamily
1P8PA 2GH6A 1XFKA 3MFWA 3LP4A 1HQHA 3SFHA 4ITYA 1WOGA 4RN1A 1PQ3A 5IWGA 5EF8A 1TBLA 3SL0A 5LI3A 4FCIA 3MJLA 4HXQA 1P8SA 4IU1A 5EF7A 4QA7A 5FUEA 3E8ZA 4A69A 2EIVA 4IU0A 4QA4A 1HQFA 4RLAA 5G17A 2V5WA 4CBTA 3F0RA 1P8OA 4Q3SA 1C3PA 4RHLA 4GWCA 1HQ5A 5G1BA 4BZ8A 2VQOA 2VQJA 4HWWA 4Q3RA 2RLAA 3Q9BA 4I06A 4GSMA 5RLAA 4Q3TA 4QA2A 4MXRA 3THJA 1WOHA 1TBJA 4Q3QA 5EEIA 5THSA 1T67A 2AEBA 2EF4A 4Q3RC 1T4PA 3EZTA 3DJ8A 5HJAA 1TBHA 3F80A 4GSZA 3RQDA 5EFKB 3F06A 3E6KA 1HQGA 3MAXA 4GSVA 2VQQA 2VQVA 3F07A 4RN0A 5G0XA 4MYKA 4Q3UA 4BKXB 5G12A 5G1CA 3MZ3A 4ZUMA 1WOIA 1T4RA 3E6VA 3PZLA 4ZUNA 3EW8A 4ZUPA 5CEVA 4IE3A 1ZPEA 3C0YA 1ZZ1A 4LXZA 5DC8A 4BZ7A 3MZ4A 3LP7A 5EEMA 1T5FA 2A0MA 5G0JA 4QA1A 1T5GA 4ZURA 3MFVA 4HZEA 4IU5A 4RN2A 4CQFA 2PHAA 1ZZ0A 5ICNB 3KV2A 5G13A 4BZ6A 5DC5A 1HQXA 3ZNSA 3C10A 1ZZ3A 4Q40A 5EEFA 5D1CA 1CEVA 4GWDA 2CEVA 4ZUOA 5HJ9A 3THEA 2ZAVA 2PHOA 4BZ9A 2VQWG 4QA0A 4IE2A 1T4SA 1T69A 1WVBA 3Q9CA 3MZ7A 3NIPA 4QA5A 3C0ZA 2VQMA 5D1BA 5EFGA 4MYLA 4IXUA 4Q41A 3MMRA 4FCKA 4Q3PA 5G10A 5FCWA 3LHLA 3THHA 1C3RA 1W22A 4Q3VA 1T64A 5G0GA 5G11A 5IX0A 5THUA 1GQ6A 3E8QA 1T4TA 4G3HA 4LY1A 5G1AA 3ZNRA 5EENA 5BWZA 1P8RA 4IE1A 1P8NA 5D1DA 5EFJD 4RHIA 5THTA 3SFFA 3M1RA 3CEVA 3NIQA 4RHKA 1ZPGA 4QA3A 3EZPA 3Q9FA 3EWFA 5EFHA 5G0YA 4DZ4A 1TA1A 1C3SA 1P8MA 5G3WA 2V5XA 4ZUQA 4IXVA 1R1OA 1VKGA 2VCGA 3NIOA 3TH7A 4BZ5A 4QA6A 3TF3A 4CEVA 5A2SA 1WVAA 5DC6A 3MZ6A 3Q9EA 4MYNA 2PLLA 5G0IA 1GQ7A 3SKKA 5JI5A 4IU4A 4MYFA 1D3VA 4Q42A 5EFBD 4CBYA 3E9BA 3GMZA 2EF5A 4RHQA 5EFNA 5G0HA 3SJTA 1RLAA 3GN0A 4RHMA 3RLAA 5EEKA 5DC7A 1P8QA 5THVA 3MENA 3SL1A 4RHJA
chains in the Genus database with same CATH topology
2GH6A 3SFHA 4RN1A 5IWGA 5EF8A 5LI3A 5FUEA 5EF7A 4QA7A 4A69A 4CBTA 4QA4A 5G17A 2V5WA 3F0RA 1C3PA 5G1BA 4BZ8A 2VQOA 2VQJA 3Q9BA 4QA2A 5THSA 5EEIA 1T67A 3EZTA 3RQDA 5EFKB 3F06A 3MAXA 2VQQA 2VQVA 3F07A 4RN0A 5G0XA 4BKXB 5G12A 5G1CA 3MZ3A 4ZUMA 4ZUNA 3EW8A 4ZUPA 3C0YA 4LXZA 1ZZ1A 5DC8A 4BZ7A 3MZ4A 5EEMA 5G0JA 4QA1A 4CQFA 4ZURA 4RN2A 1ZZ0A 5ICNB 5G13A 4BZ6A 5DC5A 3ZNSA 3C10A 1ZZ3A 5EEFA 5D1CA 4ZUOA 4BZ9A 2VQWG 4QA0A 1T69A 3Q9CA 3MZ7A 4QA5A 3C0ZA 2VQMA 5D1BA 5EFGA 5G10A 5FCWA 1C3RA 1W22A 5G11A 1T64A 5G0GA 5IX0A 5THUA 4LY1A 5G1AA 3ZNRA 5EENA 5BWZA 5EFJD 5D1DA 5THTA 3SFFA 4QA3A 3EZPA 3Q9FA 3EWFA 5EFHA 5G0YA 5G3WA 1C3SA 2V5XA 4ZUQA 4BZ5A 1VKGA 2VCGA 4QA6A 5A2SA 5DC6A 3MZ6A 3Q9EA 5G0IA 5JI5A 5EFBD 4CBYA 5G0HA 5EFNA 5EEKA 5DC7A 5THVA 3MENA
chains in the Genus database with same CATH homology


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