4A3FD

Rna polymerase ii initial transcribing complex with a 6nt dna-rna hybrid and soaked with ampcpp
Total Genus 54
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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
54
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 54
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; 4a3fD02
2JA5D 4A3GD 1Y1VD 4A93D 4A3LD 4A3ED 3PO3D 1WCMD 5IYDD 3FKID 4A3ID 4A3DD 3HOZD 4A3FD 3H3VE 1Y14A 3HOXD 2C35A 2JA6D 4A3BD 2R93D 2R7ZD 5C3ED 3HOYD 2VUMD 5C4XD 5IYBD 3H0GD 2R92D 2B63D 5IP9D 2JA8D 3PO2D 3HOVD 5IP7D 3HOUD 4BBSD 4BXXD 4A3CD 1Y1WD 4BY7D 3HOWD 5IYCD 4BY1D 3I4ND 3AYHA 2JA7D 5C44D 4BBRD 4A3JD 4A3KD 5FLMD 3I4MD 4A3MD
chains in the Genus database with same CATH superfamily
1ALUA 4A3ED 3TGXB 4DKCA 3HOYD 2CFQA 1ITIA 4IU8A 2B8XA 1BCNA 4OAAA 4QIQA 3HOWD 4JR9A 1HGUA 4A3KD 1GA3A 1M4CA 1HWGA 2L3YA 5D28B 4D2CA 2JA5D 1PVHB 2XUTA 2PSMA 1EVSA 2ERJD 5IYBD 1RW5A 3H0GD 3QB1A 2Q7NB 5KNHI 2JA8D 1FYHA 4UVMA 3I4ND 4J05A 4O6KA 1QVNA 3DLQI 1PY2A 4ZYRA 5GXBA 1RCBA 3BPLA 4NI7A 1F45B 2HYMB 3UF2A 3D48P 3WDOA 3UX9A 4LRLA 2V8NA 3UF5A 4A3JD 4A3MD 3OG6A 3BESL 3D87A 1BGCA 1V7MV 4IKYA 3S9DA 4DKEA 4U4WA 3NPZA 4TPGA 3G6DA 3PIWA 5EQGA 1B5LA 2B8ZA 1SCFA 4LEPA 3UEZE 4DKFA 2Y5YA 3LB6A 4NEMA 1BGDA 1Y1VD 3NCCA 5D71A 4A3LD 3H3VE 4RS1A 3DUHC 3N0PA 3QAZA 4XNIA 2B91A 2KZ1A 2O6IA 1FG9A 3DI2A 3HOVD 1M49A 4ZWCA 2GMFA 5FLMD 3O7QA 4MHLA 3INKC 3VA2A 4A3FD 3QB7A 4YDYI 1Y6KL 1M4AA 1ITMA 1ITLA 5D59A 1CN4C 2B63D 3PO2D 2Z3QA 5IP7D 4BBSD 4EXPA 2D9QA 4PYPA 5EQIA 2E9WC 3WCYI 4NI9A 4YB9D 1M4BA 2O26A 1Y14A 3BPOA 5FUCA 1CNT1 1PGRA 3OG4A 3QT2C 1V7NV 5IP9D 5C7XA 1BP3A 3G9VB 3BPNA 1BUYA 1HZIA 1D9CA 1P9MB 1Y1WD 1RFBA 3N06A 3EW3A 4A93D 4IU9A 3PO3D 3FKID 2OQPA 1NBPA 1HULA 1IK0A 1EMRA 5D72A 2Q98A 1ILKA 1AXIA 4EXNA 4I77Z 2INTA 4BY7D 4TPHA 4U4VA 5C44D 2H24A 2O27A 1EERA 3L5WI 1IARA 4JA3A 4PS4A 4XNJA 1AX8A 2B5IA 2C35A 1CD9A 3HOXD 2LAGA 1PW6A 2R92D 3HMXB 4NEJA 2JA7D 4BBRD 3SE4B 3L5XA 1INRA 1M47A 4A3ID 4A3DD 1PV7A 4IKVA 4YUEC 1VLKA 5C3ED 1LK3A 5E4EA 1CSGA 1IJZA 5LQBA 1ITFA 1BBNA 4GBYA 2Q14A 4YBQA 1ETEA 3I4MD 4O9HA 4TPJA 5EQHA 1Y6ML 4DKDA 1A7MA 2ILKA 1RHGA 5IYDD 4ZS7A 3NCBA 1I1RB 2CYKA 1IRLA 3HHRA 2Z3RA 3PIVA 1A22A 4NN7A 3HOUD 1YKBA 4OH3A 5IYCD 2B90A 4JREA 1EKUA 4NKQC 3NCFA 3OQ3A 4ZF7A 5D70A 1KF9A 4GRWA 5A2OA 3MZGA 2CFPA 5TS9A 3NCEA 3QWRB 3D85C 1M4RA 4A3CD 5FHXA 1LKIA 4A3GD 4IKWA 3LB6B 1N1FA 4APSA 1GNCA 5D22A 2B8UA 5C65A 4X51A 1J7VL 1JLIA 4LDSA 1M48A 1CYLA 4GC0A 4BXXD 3DI3A 4BY1D 3AYHA 3B5KA 4ZW9A 3O7PA 2XQBA 1WCMD 3HOZD 4D2BA 2IL6A 2D48A 1Y6NL 4YQXA 2R93D 2VUMD 1HUWA 1PW4A 1Z92A 4W6VA 2L3OA 1HIKA 4J4LC 4NN6A 4D2DA 1D9GA 1PV6A 4IKXA 1HWHA 4DOHA 3SE3B 1WU3I 3DGCL 1Z7CA 1EXZA 2R7ZD 4FA8E 4U4TA 4IKZA 5A2NA 4NN5A 1F6FA 5D58A 5D6KA 4ZWBA 4Q65A 4CNIC 3HHCA 4YPGC 3Q1SI 1HIJA 3IRHA 2JA6D 5L6YC 4A3BD 1AU1A 5C4XD 3EJJA 4WRLB 4Z5RD 4GS7A 2LMSA 1LQSL 2B8YA 1BGEA 1IL6A 4GBZA
chains in the Genus database with same CATH topology
4A3GD 1EERA 1Y1VD 1ALUA 3L5WI 3NCCA 1IARA 4PS4A 5D71A 3LB6B 4A3ED 1N1FA 4A3LD 3TGXB 4DKCA 1GNCA 3H3VE 1AX8A 2B5IA 2C35A 1CD9A 3DUHC 4RS1A 5D22A 2B8UA 3N0PA 3QAZA 3HOYD 2LAGA 2B91A 4X51A 1J7VL 2KZ1A 1ITIA 1JLIA 2O6IA 1PW6A 2R92D 3HMXB 1FG9A 1M48A 3DI2A 3HOVD 1CYLA 4BXXD 2B8XA 1M49A 1BCNA 4NEJA 3DI3A 3HOWD 2GMFA 4BY1D 3AYHA 1HGUA 2JA7D 4BBRD 4A3KD 5FLMD 1M4CA 1HWGA 2L3YA 3B5KA 4MHLA 5D28B 3SE4B 2JA5D 1PVHB 3INKC 3VA2A 3L5XA 1INRA 2XQBA 1M47A 1WCMD 4A3ID 4A3DD 3HOZD 4A3FD 3QB7A 4YDYI 2PSMA 2IL6A 2D48A 4YUEC 1Y6KL 1EVSA 1Y6NL 1VLKA 4YQXA 2R93D 5C3ED 2ERJD 1LK3A 2VUMD 5E4EA 1M4AA 1ITMA 1ITLA 1HUWA 1RW5A 1CN4C 3H0GD 3QB1A 2Q7NB 1Z92A 5KNHI 2B63D 2JA8D 3PO2D 1CSGA 2Z3QA 1IJZA 5IP7D 2L3OA 1HIKA 5LQBA 3HOXD 4BBSD 1FYHA 4EXPA 1ITFA 1BBNA 4J4LC 4NN6A 1D9GA 2D9QA 3I4ND 2Q14A 1ETEA 1HWHA 4DOHA 4O9HA 3SE3B 3I4MD 4O6KA 1Y6ML 2E9WC 1QVNA 3DLQI 1WU3I 3WCYI 4NI9A 3DGCL 4DKDA 1PY2A 1A7MA 2ILKA 1M4BA 1RHGA 1Z7CA 2O26A 5IYDD 1Y14A 3BPOA 5FUCA 1EXZA 1CNT1 1RCBA 3BPLA 4NI7A 1PGRA 4ZS7A 3NCBA 1F45B 1I1RB 2CYKA 3OG4A 1V7NV 2HYMB 3QT2C 4FA8E 1IRLA 2R7ZD 3UF2A 3HHRA 2Z3RA 3D48P 5IP9D 3PIVA 1A22A 1F6FA 4NN5A 4NN7A 3UX9A 5C7XA 1BP3A 3G9VB 4LRLA 1YKBA 3HOUD 3BPNA 1BUYA 1HZIA 1D9CA 1P9MB 1Y1WD 4CNIC 5IYCD 5IYBD 2B90A 1RFBA 3UF5A 3N06A 4A3JD 1EKUA 3HHCA 4YPGC 4NKQC 3EW3A 4A3MD 3Q1SI 3OG6A 4A93D 3BESL 1HIJA 3PO3D 3D87A 1BGCA 1V7MV 3FKID 3IRHA 3NCFA 3S9DA 2OQPA 1NBPA 3OQ3A 4ZF7A 4DKEA 2JA6D 5D70A 5L6YC 4A3BD 1AU1A 1KF9A 5C4XD 1HULA 1IK0A 3NPZA 4GRWA 1EMRA 3MZGA 3EJJA 3G6DA 4WRLB 3PIWA 4Z5RD 5TS9A 4GS7A 5D72A 2Q98A 1B5LA 2B8ZA 2LMSA 1SCFA 1ILKA 1AXIA 3NCEA 1LQSL 2B8YA 3QWRB 4EXNA 4I77Z 2INTA 3D85C 3UEZE 1M4RA 4A3CD 4DKFA 1BGEA 3LB6A 1GA3A 1IL6A 4BY7D 4NEMA 5C44D 1BGDA 2H24A 2O27A 5FHXA 1LKIA
chains in the Genus database with same CATH homology


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