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


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