5FLMD

Structure of transcribing mammalian rna polymerase ii
Total Genus 43
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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
43
sequence length
128
structure length
128
Chain Sequence
EEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQ
Loading diagram...

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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publication title Structure of Transcribing Mammalian RNA Polymerase II
pubmed doi rcsb
molecule keywords DNA-DIRECTED RNA POLYMERASE
molecule tags Transcription
total genus 43
structure length 128
sequence length 128
ec nomenclature
pdb deposition date 2015-10-26

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D PF03874 RNA_pol_Rpb4 RNA polymerase Rpb4
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.20.1250.40 Mainly Alpha Up-down Bundle Growth Hormone; Chain: A; Growth Hormone; Chain: A; 5flmD00
4BY1D 2R93D 4BXXD 5IYDD 4A3DD 3HOYD 4A3GD 3FKID 2JA6D 2JA7D 3HOZD 2R7ZD 3AYHA 4A3ID 4A3KD 3H0GD 5C3ED 1Y14A 4A93D 2JA5D 5C44D 2R92D 4BBRD 3H3VE 4A3CD 4BBSD 3HOWD 5IYCD 3I4MD 2B63D 4A3FD 4A3JD 2VUMD 5IP9D 3PO2D 3HOUD 1WCMD 3HOXD 5IYBD 1Y1VD 5C4XD 4A3LD 4A3MD 5IP7D 2C35A 3I4ND 1Y1WD 2JA8D 4A3BD 4BY7D 3HOVD 3PO3D 5FLMD 4A3ED
chains in the Genus database with same CATH superfamily
4BY1D 4NI7A 2O26A 2XQBA 1RFBA 3DI3A 4A3CD 4DOHA 1YKBA 1CD9A 1JLIA 1M4AA 4U4VA 1Y6KL 1RCBA 5D22A 3UX9A 1IJZA 3QAZA 2KZ1A 2ERJD 4EXPA 1AU1A 5FUCA 4J4LC 3I4MD 4X51A 1M4RA 1IL6A 2Z3QA 1CN4C 3SE3B 1P9MB 1ETEA 1EMRA 2JA8D 3N0PA 1IARA 5D72A 5D28B 3BESL 2Q14A 4DKFA 4A3GD 3AYHA 3EW3A 2OQPA 5L6YC 3DLQI 3INKC 4IKZA 1GA3A 4A3JD 1ITFA 4DKCA 2B8ZA 3PO3D 1J7VL 4BXXD 1ITMA 2JA7D 2XUTA 1V7MV 4NKQC 4WRLB 4YUEC 2Q98A 4GBZA 3QB1A 2C35A 1ITIA 1BP3A 4U4WA 1D9GA 5EQHA 3O7QA 1INRA 5LQBA 1HULA 4DKDA 2R92D 1A22A 4TPJA 3HOWD 4A3FD 2VUMD 2D48A 3NPZA 3N06A 4PYPA 4OH3A 4ZYRA 3PIWA 4D2BA 3HOVD 4GS7A 1HUWA 1NBPA 4IKXA 3HOZD 4IKYA 5C7XA 3OG4A 4BBRD 4NEJA 3D87A 3HHCA 1A7MA 2LMSA 1QVNA 1M48A 1PW6A 1FG9A 3DGCL 3HOXD 4Z5RD 2ILKA 3QWRB 2H24A 3QT2C 1V7NV 5E4EA 4YDYI 4YPGC 2R7ZD 5D6KA 2GMFA 5D71A 1M49A 3BPLA 5IP9D 4JREA 4NN6A 3NCBA 4A3MD 1KF9A 3NCCA 4GRWA 4LDSA 3LB6B 1PV6A 3QB7A 2CYKA 3HHRA 2B8YA 4IKWA 1VLKA 2Y5YA 5D59A 1PV7A 1WCMD 3DI2A 4D2CA 3S9DA 5IYBD 5IP7D 4IKVA 1M4BA 3WDOA 3IRHA 5TS9A 5C44D 1CSGA 3PO2D 4IU8A 3PIVA 1BGDA 5FHXA 4O9HA 5C4XD 4GC0A 2B8UA 1EXZA 2L3OA 1RHGA 2B8XA 1HZIA 1LKIA 2E9WC 1F6FA 5D70A 3LB6A 1M4CA 5A2OA 4XNIA 4YB9D 4JA3A 5EQIA 4ZW9A 2Q7NB 2V8NA 1Y6ML 4A3LD 3I4ND 2LAGA 4A3BD 1BBNA 1IRLA 4U4TA 1BCNA 4TPHA 4YBQA 5GXBA 3DUHC 3OQ3A 4A3KD 2CFPA 4ZWCA 5IYCD 1Z92A 1Y6NL 1GNCA 4XNJA 4MHLA 1LK3A 5D58A 1HIKA 3NCEA 4NN5A 4A3ED 1HWHA 3B5KA 3SE4B 3OG6A 3HOYD 1AX8A 4DKEA 4GBYA 4IU9A 4A3ID 3EJJA 5C3ED 3G9VB 1LQSL 2HYMB 4APSA 1CYLA 2PSMA 1HGUA 1N1FA 3UF2A 1ALUA 4LRLA 1Y1WD 2IL6A 3HMXB 4JR9A 3BPOA 5FLMD 5C65A 1FYHA 3Q1SI 1D9CA 1CNT1 1EKUA 1Z7CA 3H0GD 4TPGA 4EXNA 4OAAA 1BGCA 2JA5D 4ZS7A 4UVMA 2B63D 2O6IA 3UF5A 4ZWBA 1SCFA 4QIQA 4W6VA 1WU3I 1EERA 3L5XA 1PW4A 4Q65A 5A2NA 1RW5A 3FKID 3TGXB 4FA8E 2INTA 4LEPA 4A93D 2O27A 1ILKA 2B90A 1BGEA 2B91A 1IK0A 1EVSA 3L5WI 1Y1VD 1HWGA 4RS1A 4NI9A 1AXIA 2D9QA 2CFQA 4NEMA 3D85C 3BPNA 1HIJA 4YQXA 1BUYA 1F45B 4PS4A 1Y14A 4ZF7A 3H3VE 4BBSD 5KNHI 3HOUD 2L3YA 5EQGA 1ITLA 3G6DA 4BY7D 1PGRA 2R93D 4D2DA 3O7PA 5IYDD 4A3DD 4O6KA 2JA6D 1I1RB 3NCFA 1PVHB 3VA2A 1B5LA 2Z3RA 4CNIC 1M47A 1PY2A 3MZGA 4I77Z 3D48P 4NN7A 3UEZE 3WCYI 4J05A 2B5IA
chains in the Genus database with same CATH topology
4BY1D 1M4BA 1INRA 3Q1SI 5LQBA 1D9CA 4NI7A 1CNT1 1HULA 2O26A 1EKUA 2XQBA 1Z7CA 3H0GD 4EXNA 1BGCA 1RFBA 3IRHA 4DKDA 2JA5D 5TS9A 5C44D 2R92D 4ZS7A 3DI3A 4A3CD 1A22A 4DOHA 3HOWD 1YKBA 2B63D 1CSGA 2O6IA 4A3FD 3UF5A 2VUMD 1CD9A 3PO2D 2D48A 3BPOA 1JLIA 1M4AA 1SCFA 3NPZA 3PIVA 3N06A 1WU3I 1BGDA 5FHXA 1EERA 4O9HA 3L5XA 5C4XD 1Y6KL 2B8UA 1RCBA 3PIWA 5D22A 3UX9A 1EXZA 1IJZA 2L3OA 3HOVD 4GS7A 1RHGA 2B8XA 3QAZA 1HUWA 1NBPA 1RW5A 1HZIA 2KZ1A 2ERJD 1LKIA 2E9WC 4EXPA 1F6FA 5D70A 3FKID 3TGXB 3HOZD 4FA8E 1AU1A 3LB6A 2INTA 5FUCA 1M4CA 5C7XA 4A93D 3OG4A 2O27A 4BBRD 1ILKA 4J4LC 2B90A 3I4MD 1BGEA 2B91A 4X51A 4NEJA 1IK0A 3D87A 3HHCA 1M4RA 1A7MA 1EVSA 2LMSA 2Q7NB 1IL6A 1QVNA 1CN4C 2Z3QA 3SE3B 1P9MB 1ETEA 1M48A 1PW6A 1Y6ML 1FG9A 1Y1VD 1HWGA 3DGCL 3L5WI 1EMRA 4RS1A 3HOXD 4Z5RD 4NI9A 3I4ND 4A3LD 1AXIA 2JA8D 2LAGA 2D9QA 1BBNA 3N0PA 1IRLA 2ILKA 1IARA 3QWRB 4A3BD 4NEMA 5D72A 3D85C 5D28B 1BCNA 3BESL 2H24A 2Q14A 3QT2C 1V7NV 3BPNA 5E4EA 4YDYI 4DKFA 1HIJA 3DUHC 4A3GD 4YPGC 2R7ZD 3AYHA 4YQXA 3EW3A 3OQ3A 4A3KD 2OQPA 2GMFA 1BUYA 1F45B 4PS4A 1Y14A 3DLQI 5D71A 4ZF7A 5L6YC 3INKC 1M49A 3BPLA 3H3VE 4BBSD 5IYCD 1GA3A 1Z92A 4A3JD 5KNHI 5IP9D 1Y6NL 1GNCA 1ITFA 3HOUD 4NN6A 4MHLA 2L3YA 1LK3A 3NCBA 4A3MD 4DKCA 1KF9A 1HIKA 1ITLA 3G6DA 4BY7D 3NCEA 3NCCA 2B8ZA 4GRWA 3PO3D 4NN5A 1PGRA 4A3ED 1J7VL 3LB6B 2R93D 1HWHA 3B5KA 3SE4B 5IYDD 4BXXD 3OG6A 4O6KA 3HOYD 1ITMA 4A3DD 1AX8A 3QB7A 4DKEA 2JA6D 2JA7D 1I1RB 3NCFA 3EJJA 1PVHB 3VA2A 4A3ID 1B5LA 5C3ED 3G9VB 2CYKA 1V7MV 2Z3RA 3HHRA 4NKQC 1LQSL 4CNIC 2B8YA 1M47A 1PY2A 2HYMB 3MZGA 1CYLA 2PSMA 4I77Z 1HGUA 3D48P 1N1FA 4NN7A 1VLKA 1ALUA 4WRLB 4YUEC 3UEZE 3UF2A 1WCMD 2Q98A 3DI2A 3WCYI 3S9DA 5IYBD 4LRLA 3QB1A 5IP7D 2C35A 1Y1WD 1ITIA 1BP3A 2IL6A 3HMXB 1D9GA 2B5IA 5FLMD 1FYHA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4BY1 D;  2R93 D;  4BXX D;  5IYD D;  4A3D D;  3HOY D;  4A3G D;  3FKI D;  2JA6 D;  2JA7 D;  3HOZ D;  2R7Z D;  3AYH A;  4A3I D;  4A3K D;  3H0G D;  5C3E D;  1Y14 A;  4A93 D;  2JA5 D;  5C44 D;  2R92 D;  4BBR D;  3H3V E;  4A3C D;  4BBS D;  3HOW D;  5IYC D;  3I4M D;  2B63 D;  4A3F D;  4A3J D;  2VUM D;  5IP9 D;  3PO2 D;  3HOU D;  1WCM D;  3HOX D;  5IYB D;  1Y1V D;  5C4X D;  4A3L D;  4A3M D;  5IP7 D;  2C35 A;  3I4N D;  1Y1W D;  2JA8 D;  4A3B D;  4BY7 D;  3HOV D;  3PO3 D;  5FLM D;  4A3E D; 
#chains in the Genus database with same CATH topology
 4BY1 D;  4NI7 A;  2O26 A;  2XQB A;  1RFB A;  3DI3 A;  4A3C D;  4DOH A;  1YKB A;  1CD9 A;  1JLI A;  1M4A A;  4U4V A;  1Y6K L;  1RCB A;  5D22 A;  3UX9 A;  1IJZ A;  3QAZ A;  2KZ1 A;  2ERJ D;  4EXP A;  1AU1 A;  5FUC A;  4J4L C;  3I4M D;  4X51 A;  1M4R A;  1IL6 A;  2Z3Q A;  1CN4 C;  3SE3 B;  1P9M B;  1ETE A;  1EMR A;  2JA8 D;  3N0P A;  1IAR A;  5D72 A;  5D28 B;  3BES L;  2Q14 A;  4DKF A;  4A3G D;  3AYH A;  3EW3 A;  2OQP A;  5L6Y C;  3DLQ I;  3INK C;  4IKZ A;  1GA3 A;  4A3J D;  1ITF A;  4DKC A;  2B8Z A;  3PO3 D;  1J7V L;  4BXX D;  1ITM A;  2JA7 D;  2XUT A;  1V7M V;  4NKQ C;  4WRL B;  4YUE C;  2Q98 A;  4GBZ A;  3QB1 A;  2C35 A;  1ITI A;  1BP3 A;  4U4W A;  1D9G A;  5EQH A;  3O7Q A;  1INR A;  5LQB A;  1HUL A;  4DKD A;  2R92 D;  1A22 A;  4TPJ A;  3HOW D;  4A3F D;  2VUM D;  2D48 A;  3NPZ A;  3N06 A;  4PYP A;  4OH3 A;  4ZYR A;  3PIW A;  4D2B A;  3HOV D;  4GS7 A;  1HUW A;  1NBP A;  4IKX A;  3HOZ D;  4IKY A;  5C7X A;  3OG4 A;  4BBR D;  4NEJ A;  3D87 A;  3HHC A;  1A7M A;  2LMS A;  1QVN A;  1M48 A;  1PW6 A;  1FG9 A;  3DGC L;  3HOX D;  4Z5R D;  2ILK A;  3QWR B;  2H24 A;  3QT2 C;  1V7N V;  5E4E A;  4YDY I;  4YPG C;  2R7Z D;  5D6K A;  2GMF A;  5D71 A;  1M49 A;  3BPL A;  5IP9 D;  4JRE A;  4NN6 A;  3NCB A;  4A3M D;  1KF9 A;  3NCC A;  4GRW A;  4LDS A;  3LB6 B;  1PV6 A;  3QB7 A;  2CYK A;  3HHR A;  2B8Y A;  4IKW A;  1VLK A;  2Y5Y A;  5D59 A;  1PV7 A;  1WCM D;  3DI2 A;  4D2C A;  3S9D A;  5IYB D;  5IP7 D;  4IKV A;  1M4B A;  3WDO A;  3IRH A;  5TS9 A;  5C44 D;  1CSG A;  3PO2 D;  4IU8 A;  3PIV A;  1BGD A;  5FHX A;  4O9H A;  5C4X D;  4GC0 A;  2B8U A;  1EXZ A;  2L3O A;  1RHG A;  2B8X A;  1HZI A;  1LKI A;  2E9W C;  1F6F A;  5D70 A;  3LB6 A;  1M4C A;  5A2O A;  4XNI A;  4YB9 D;  4JA3 A;  5EQI A;  4ZW9 A;  2Q7N B;  2V8N A;  1Y6M L;  4A3L D;  3I4N D;  2LAG A;  4A3B D;  1BBN A;  1IRL A;  4U4T A;  1BCN A;  4TPH A;  4YBQ A;  5GXB A;  3DUH C;  3OQ3 A;  4A3K D;  2CFP A;  4ZWC A;  5IYC D;  1Z92 A;  1Y6N L;  1GNC A;  4XNJ A;  4MHL A;  1LK3 A;  5D58 A;  1HIK A;  3NCE A;  4NN5 A;  4A3E D;  1HWH A;  3B5K A;  3SE4 B;  3OG6 A;  3HOY D;  1AX8 A;  4DKE A;  4GBY A;  4IU9 A;  4A3I D;  3EJJ A;  5C3E D;  3G9V B;  1LQS L;  2HYM B;  4APS A;  1CYL A;  2PSM A;  1HGU A;  1N1F A;  3UF2 A;  1ALU A;  4LRL A;  1Y1W D;  2IL6 A;  3HMX B;  4JR9 A;  3BPO A;  5FLM D;  5C65 A;  1FYH A;  3Q1S I;  1D9C A;  1CNT 1;  1EKU A;  1Z7C A;  3H0G D;  4TPG A;  4EXN A;  4OAA A;  1BGC A;  2JA5 D;  4ZS7 A;  4UVM A;  2B63 D;  2O6I A;  3UF5 A;  4ZWB A;  1SCF A;  4QIQ A;  4W6V A;  1WU3 I;  1EER A;  3L5X A;  1PW4 A;  4Q65 A;  5A2N A;  1RW5 A;  3FKI D;  3TGX B;  4FA8 E;  2INT A;  4LEP A;  4A93 D;  2O27 A;  1ILK A;  2B90 A;  1BGE A;  2B91 A;  1IK0 A;  1EVS A;  3L5W I;  1Y1V D;  1HWG A;  4RS1 A;  4NI9 A;  1AXI A;  2D9Q A;  2CFQ A;  4NEM A;  3D85 C;  3BPN A;  1HIJ A;  4YQX A;  1BUY A;  1F45 B;  4PS4 A;  1Y14 A;  4ZF7 A;  3H3V E;  4BBS D;  5KNH I;  3HOU D;  2L3Y A;  5EQG A;  1ITL A;  3G6D A;  4BY7 D;  1PGR A;  2R93 D;  4D2D A;  3O7P A;  5IYD D;  4A3D D;  4O6K A;  2JA6 D;  1I1R B;  3NCF A;  1PVH B;  3VA2 A;  1B5L A;  2Z3R A;  4CNI C;  1M47 A;  1PY2 A;  3MZG A;  4I77 Z;  3D48 P;  4NN7 A;  3UEZ E;  3WCY I;  4J05 A;  2B5I A; 
#chains in the Genus database with same CATH homology
 4BY1 D;  1M4B A;  1INR A;  3Q1S I;  5LQB A;  1D9C A;  4NI7 A;  1CNT 1;  1HUL A;  2O26 A;  1EKU A;  2XQB A;  1Z7C A;  3H0G D;  4EXN A;  1BGC A;  1RFB A;  3IRH A;  4DKD A;  2JA5 D;  5TS9 A;  5C44 D;  2R92 D;  4ZS7 A;  3DI3 A;  4A3C D;  1A22 A;  4DOH A;  3HOW D;  1YKB A;  2B63 D;  1CSG A;  2O6I A;  4A3F D;  3UF5 A;  2VUM D;  1CD9 A;  3PO2 D;  2D48 A;  3BPO A;  1JLI A;  1M4A A;  1SCF A;  3NPZ A;  3PIV A;  3N06 A;  1WU3 I;  1BGD A;  5FHX A;  1EER A;  4O9H A;  3L5X A;  5C4X D;  1Y6K L;  2B8U A;  1RCB A;  3PIW A;  5D22 A;  3UX9 A;  1EXZ A;  1IJZ A;  2L3O A;  3HOV D;  4GS7 A;  1RHG A;  2B8X A;  3QAZ A;  1HUW A;  1NBP A;  1RW5 A;  1HZI A;  2KZ1 A;  2ERJ D;  1LKI A;  2E9W C;  4EXP A;  1F6F A;  5D70 A;  3FKI D;  3TGX B;  3HOZ D;  4FA8 E;  1AU1 A;  3LB6 A;  2INT A;  5FUC A;  1M4C A;  5C7X A;  4A93 D;  3OG4 A;  2O27 A;  4BBR D;  1ILK A;  4J4L C;  2B90 A;  3I4M D;  1BGE A;  2B91 A;  4X51 A;  4NEJ A;  1IK0 A;  3D87 A;  3HHC A;  1M4R A;  1A7M A;  1EVS A;  2LMS A;  2Q7N B;  1IL6 A;  1QVN A;  1CN4 C;  2Z3Q A;  3SE3 B;  1P9M B;  1ETE A;  1M48 A;  1PW6 A;  1Y6M L;  1FG9 A;  1Y1V D;  1HWG A;  3DGC L;  3L5W I;  1EMR A;  4RS1 A;  3HOX D;  4Z5R D;  4NI9 A;  3I4N D;  4A3L D;  1AXI A;  2JA8 D;  2LAG A;  2D9Q A;  1BBN A;  3N0P A;  1IRL A;  2ILK A;  1IAR A;  3QWR B;  4A3B D;  4NEM A;  5D72 A;  3D85 C;  5D28 B;  1BCN A;  3BES L;  2H24 A;  2Q14 A;  3QT2 C;  1V7N V;  3BPN A;  5E4E A;  4YDY I;  4DKF A;  1HIJ A;  3DUH C;  4A3G D;  4YPG C;  2R7Z D;  3AYH A;  4YQX A;  3EW3 A;  3OQ3 A;  4A3K D;  2OQP A;  2GMF A;  1BUY A;  1F45 B;  4PS4 A;  1Y14 A;  3DLQ I;  5D71 A;  4ZF7 A;  5L6Y C;  3INK C;  1M49 A;  3BPL A;  3H3V E;  4BBS D;  5IYC D;  1GA3 A;  1Z92 A;  4A3J D;  5KNH I;  5IP9 D;  1Y6N L;  1GNC A;  1ITF A;  3HOU D;  4NN6 A;  4MHL A;  2L3Y A;  1LK3 A;  3NCB A;  4A3M D;  4DKC A;  1KF9 A;  1HIK A;  1ITL A;  3G6D A;  4BY7 D;  3NCE A;  3NCC A;  2B8Z A;  4GRW A;  3PO3 D;  4NN5 A;  1PGR A;  4A3E D;  1J7V L;  3LB6 B;  2R93 D;  1HWH A;  3B5K A;  3SE4 B;  5IYD D;  4BXX D;  3OG6 A;  4O6K A;  3HOY D;  1ITM A;  4A3D D;  1AX8 A;  3QB7 A;  4DKE A;  2JA6 D;  2JA7 D;  1I1R B;  3NCF A;  3EJJ A;  1PVH B;  3VA2 A;  4A3I D;  1B5L A;  5C3E D;  3G9V B;  2CYK A;  1V7M V;  2Z3R A;  3HHR A;  4NKQ C;  1LQS L;  4CNI C;  2B8Y A;  1M47 A;  1PY2 A;  2HYM B;  3MZG A;  1CYL A;  2PSM A;  4I77 Z;  1HGU A;  3D48 P;  1N1F A;  4NN7 A;  1VLK A;  1ALU A;  4WRL B;  4YUE C;  3UEZ E;  3UF2 A;  1WCM D;  2Q98 A;  3DI2 A;  3WCY I;  3S9D A;  5IYB D;  4LRL A;  3QB1 A;  5IP7 D;  2C35 A;  1Y1W D;  1ITI A;  1BP3 A;  2IL6 A;  3HMX B;  1D9G A;  2B5I A;  5FLM D;  1FYH 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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