4A3ED

Rna polymerase ii initial transcribing complex with a 5nt dna-rna hybrid and soaked with ampcpp
Total Genus 53
Loading diagram...

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
53
sequence length
219
structure length
178
Chain Sequence
VSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
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 II SUBUNIT RPB1
publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
total genus 53
structure length 178
sequence length 219
ec nomenclature
pdb deposition date 2011-09-30

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; 4a3eD02
3H3VE 4A3JD 4A3LD 5C44D 3AYHA 2JA5D 2R92D 4BBSD 3HOXD 4A3ED 4A3KD 3HOYD 2B63D 4A3CD 5FLMD 4A93D 2JA8D 5IYDD 4BY7D 3H0GD 3I4MD 3I4ND 2R7ZD 2R93D 4BBRD 1Y1VD 2JA6D 4A3FD 2JA7D 5C4XD 1Y14A 5IP7D 4A3MD 4A3DD 4A3ID 4A3GD 2C35A 3PO3D 4A3BD 4BY1D 5IP9D 3PO2D 5IYBD 3HOUD 4BXXD 5C3ED 5IYCD 3HOWD 3HOZD 3HOVD 2VUMD 3FKID 1WCMD 1Y1WD
chains in the Genus database with same CATH superfamily
4PYPA 4ZWBA 4A3ED 4LEPA 1PV6A 4YUEC 5TS9A 4YPGC 4YQXA 1J7VL 3PIVA 3BPLA 4IKZA 1HUWA 4ZW9A 1CNT1 4WRLB 4BXXD 1HZIA 4Z5RD 2Y5YA 3QWRB 3BPNA 1GNCA 2CYKA 1LKIA 4DOHA 4IKXA 4OH3A 1RCBA 4IKYA 4XNIA 1ITMA 5LQBA 1NBPA 3D87A 3HOVD 1FYHA 1FG9A 1BUYA 4DKEA 3SE3B 1YKBA 2Q98A 1RHGA 4EXPA 4U4TA 4GBYA 1HWHA 3EJJA 1F45B 1BCNA 5D58A 2O6IA 3DI3A 5E4EA 1IARA 3HMXB 3G6DA 2JA5D 1D9CA 3HOYD 3SE4B 3INKC 4PS4A 2LAGA 2D48A 4D2CA 2HYMB 4DKDA 4Q65A 4U4WA 3EW3A 3HOZD 1RFBA 1JLIA 1WCMD 1BGDA 4A3JD 1D9GA 2LMSA 3UF5A 1M47A 4BY7D 3H0GD 1HWGA 4BBRD 5D71A 1A7MA 1EKUA 2XUTA 3OG4A 3H3VE 1KF9A 2Q7NB 4TPJA 3NCEA 2JA6D 2ERJD 1HIJA 4X51A 1BGEA 3WDOA 4A3BD 2B8UA 3DLQI 5IYBD 4NN6A 1BP3A 5FHXA 3UX9A 4TPGA 1Y6NL 2GMFA 1Z92A 4CNIC 2CFQA 4DKFA 4LRLA 5D72A 2R93D 3TGXB 2PSMA 4A3FD 4TPHA 4A3DD 4A3ID 1M4RA 3OG6A 3WCYI 1M4BA 1M4AA 4NEMA 4XNJA 3LB6A 3NCBA 4GC0A 3B5KA 1SCFA 1HULA 5D22A 3VA2A 5EQIA 2L3OA 1PV7A 1EVSA 1V7MV 2IL6A 2JA7D 5IP7D 3S9DA 3QT2C 2C35A 2B8YA 5FUCA 5IYCD 3HOWD 4O9HA 1PGRA 1IK0A 3DGCL 3HHCA 2B91A 4RS1A 1EMRA 4NI7A 4ZYRA 1CN4C 3N06A 2V8NA 3NPZA 2B8XA 4IKWA 1M48A 3L5XA 5C3ED 4J05A 3L5WI 3PIWA 4A3LD 5C44D 4ZS7A 4NI9A 4YBQA 1ILKA 2OQPA 5EQHA 1AXIA 1VLKA 5IYDD 5KNHI 3O7PA 3IRHA 1HGUA 5D6KA 4A3GD 2B8ZA 4U4VA 3MZGA 1M49A 1Y1WD 1I1RB 2O27A 4BBSD 1BGCA 4A3CD 5FLMD 4A93D 3N0PA 4IKVA 3I4MD 4D2BA 2ILKA 4JR9A 4O6KA 1HIKA 3OQ3A 3HOUD 1ITFA 4EXNA 1PY2A 2VUMD 1EERA 4LDSA 5GXBA 2INTA 3D85C 5C7XA 2B63D 2B90A 3DUHC 1IJZA 4APSA 5EQGA 3I4ND 5C65A 1CD9A 4IU8A 1N1FA 1PW6A 1EXZA 3Q1SI 3G9VB 4ZF7A 3QAZA 4NN7A 3UEZE 4D2DA 3PO3D 1BBNA 1A22A 1AU1A 4NKQC 3QB7A 4NN5A 2XQBA 3AYHA 2R92D 3QB1A 3HOXD 3O7QA 1V7NV 2Z3RA 1LK3A 2H24A 2L3YA 1Y1VD 5D59A 1INRA 1B5LA 4IU9A 5C4XD 1Z7CA 4YB9D 1WU3I 4MHLA 1ALUA 4A3KD 4JA3A 2R7ZD 4GBZA 4JREA 2B5IA 4J4LC 1Y14A 4YDYI 1Y6KL 4GS7A 2O26A 1M4CA 1GA3A 2E9WC 5A2OA 5D28B 4A3MD 1QVNA 1CYLA 3BESL 4ZWCA 5L6YC 3UF2A 1PW4A 3HHRA 1ETEA 1Y6ML 4I77Z 1CSGA 1RW5A 1P9MB 3D48P 4OAAA 3LB6B 1AX8A 5D70A 1IL6A 3BPOA 1LQSL 1ITLA 4DKCA 2Z3QA 3NCCA 5A2NA 1IRLA 3DI2A 2CFPA 2KZ1A 2Q14A 2D9QA 2JA8D 1F6FA 3NCFA 1PVHB 4QIQA 4GRWA 4NEJA 1ITIA 4W6VA 4FA8E 4BY1D 5IP9D 3PO2D 4UVMA 3FKID
chains in the Genus database with same CATH topology
3QB7A 4NN5A 1BGDA 4A3JD 1D9GA 2XQBA 3AYHA 2R92D 3QB1A 3DGCL 3HOXD 3HHCA 2B91A 4RS1A 1EMRA 4NI7A 4A3ED 2LMSA 3UF5A 1V7NV 1M47A 4BY7D 1CN4C 3H0GD 4YUEC 1HWGA 3N06A 2Z3RA 1LK3A 4BBRD 2H24A 2L3YA 5TS9A 1Y1VD 5D71A 1INRA 1B5LA 1A7MA 4YPGC 5C4XD 3NPZA 2B8XA 1J7VL 4YQXA 1Z7CA 1EKUA 3BPLA 3PIVA 1M48A 1HUWA 1CNT1 4WRLB 1WU3I 3OG4A 3L5XA 4BXXD 5C3ED 3L5WI 2JA8D 1HZIA 3PIWA 4Z5RD 3H3VE 4A3LD 4MHLA 5C44D 4ZS7A 4NI9A 1KF9A 3QWRB 1ILKA 1ALUA 3BPNA 2OQPA 4A3KD 1GNCA 1AXIA 1VLKA 5IYDD 2CYKA 1LKIA 2R7ZD 4DOHA 2Q7NB 5KNHI 2B5IA 3IRHA 3NCEA 4J4LC 2JA6D 1RCBA 1Y14A 2ERJD 1HIJA 1Y6KL 4YDYI 4GS7A 4X51A 2O26A 3FKID 1HGUA 1M4CA 4A3GD 1GA3A 1BGEA 2B8ZA 2E9WC 4A3BD 2B8UA 1ITMA 3DLQI 5IYBD 5LQBA 1NBPA 3D87A 3HOVD 1FYHA 1FG9A 5D28B 3MZGA 4A3MD 1M49A 1BUYA 4DKEA 1Y1WD 4NN6A 1I1RB 1QVNA 2O27A 4BBSD 3BESL 1YKBA 1BP3A 3SE3B 1BGCA 5FHXA 1CYLA 3UX9A 1IK0A 2Q98A 1RHGA 1Y6NL 2GMFA 4A3CD 1Z92A 5L6YC 4CNIC 5FLMD 3UF2A 4A93D 3N0PA 4EXPA 3HHRA 1ETEA 4DKFA 4LRLA 5D72A 3I4MD 2R93D 1Y6ML 4I77Z 3TGXB 2ILKA 1CSGA 1HWHA 2PSMA 1RW5A 1P9MB 3EJJA 4O6KA 4A3FD 1F45B 1HIKA 4A3DD 4A3ID 3D48P 1BCNA 3OQ3A 1M4RA 2O6IA 3LB6B 3HOUD 1ITFA 1AX8A 4EXNA 5D70A 3OG6A 1IL6A 1PY2A 3BPOA 3DI3A 5E4EA 1LQSL 2VUMD 1IARA 1EERA 3WCYI 1M4BA 1ITLA 3HMXB 4DKCA 1M4AA 4NEMA 3G6DA 2JA5D 2Z3QA 3NCCA 1D9CA 3LB6A 3NCBA 2INTA 1IRLA 3D85C 3DI2A 5C7XA 2KZ1A 3B5KA 2Q14A 3HOYD 1SCFA 2B90A 2B63D 1HULA 2D9QA 3DUHC 1IJZA 1F6FA 1PVHB 3NCFA 5D22A 3SE4B 3VA2A 3I4ND 3INKC 1CD9A 4GRWA 4NEJA 4PS4A 2L3OA 2LAGA 1N1FA 1PW6A 1EXZA 1EVSA 3Q1SI 1V7MV 3G9VB 2IL6A 2JA7D 5IP7D 4ZF7A 3QAZA 3S9DA 1ITIA 2D48A 4NN7A 3UEZE 2HYMB 3QT2C 2C35A 4DKDA 4FA8E 1BBNA 3PO3D 4BY1D 5IP9D 3PO2D 1A22A 2B8YA 3EW3A 5FUCA 5IYCD 3HOWD 3HOZD 1RFBA 1JLIA 1AU1A 1WCMD 4NKQC 4O9HA 1PGRA
chains in the Genus database with same CATH homology


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