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


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