4A3JD

Rna polymerase ii initial transcribing complex with a 2nt dna-rna hybrid and soaked with gmpcpp
Total Genus 49
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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
49
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 49
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; 4a3jD02
5C4XD 3HOXD 4A3BD 4BY7D 1Y14A 3PO2D 1Y1VD 2R92D 2B63D 4A3MD 2JA6D 2R7ZD 4A3FD 3PO3D 1Y1WD 4A3ED 3HOWD 5IP7D 5IYDD 4A3DD 4A3JD 4A3CD 3I4MD 3AYHA 5IP9D 5C3ED 4BXXD 5C44D 2JA5D 2VUMD 4A3KD 4A93D 4BBSD 2R93D 4BBRD 2C35A 5IYBD 3H0GD 4A3GD 4A3ID 3H3VE 4A3LD 2JA8D 3HOVD 5IYCD 3HOZD 4BY1D 3FKID 3HOYD 5FLMD 3HOUD 1WCMD 2JA7D 3I4ND
chains in the Genus database with same CATH superfamily
5C4XD 4NEJA 5D58A 1BCNA 5E4EA 1PW4A 2LAGA 3BPNA 1Y1WD 5D59A 3QT2C 3INKC 1P9MB 5C3ED 4GC0A 2Q14A 1ITFA 2C35A 4YB9D 5EQIA 4MHLA 4NN6A 3QAZA 1FYHA 2B8UA 1ETEA 3LB6A 1RW5A 2Q7NB 1LKIA 4U4TA 4A3ID 2L3OA 4NEMA 1B5LA 3G9VB 4RS1A 3I4ND 3EJJA 1HIKA 5KNHI 2L3YA 5LQBA 5C7XA 5GXBA 1GA3A 4LDSA 1D9GA 1F45B 5IP9D 4EXPA 3H0GD 4A3LD 4O9HA 5EQHA 1PVHB 5D70A 3UX9A 4ZF7A 3BPLA 1IARA 2CYKA 1INRA 1EVSA 4NKQC 2R92D 1NBPA 4YDYI 3HMXB 4DKEA 3TGXB 1HGUA 4EXNA 3HOWD 3N0PA 1EXZA 3NCCA 1ALUA 3MZGA 3OQ3A 2R93D 1Z92A 2VUMD 1RHGA 4XNJA 1IK0A 1AX8A 1JLIA 1V7NV 2Y5YA 1HUWA 5D6KA 5FHXA 4A3DD 1V7MV 4A3CD 4BXXD 3NCFA 1PY2A 1Y6KL 1QVNA 1IL6A 4BY1D 4ZW9A 3DLQI 3OG6A 1WCMD 4OAAA 4O6KA 3D85C 4A3BD 1SCFA 2KZ1A 2B8YA 3BESL 3O7PA 4TPJA 1CYLA 1N1FA 3UF5A 2OQPA 1BGEA 4IU9A 1FG9A 4JREA 2GMFA 4A3KD 4BBSD 1M4BA 1ITLA 5IYCD 1ILKA 1AU1A 3FKID 1CSGA 4GS7A 1RCBA 3B5KA 1EERA 3QB7A 2R7ZD 4DOHA 3PO3D 4A3ED 2PSMA 4A3JD 4YUEC 1M49A 4A93D 3WDOA 1PV7A 1AXIA 3HOYD 4NN5A 4NN7A 4XNIA 3DGCL 3PIVA 3N06A 3PO2D 4PYPA 2B63D 4NI9A 1VLKA 5D28B 2XQBA 1ITIA 2ERJD 4FA8E 3I4MD 1A7MA 3LB6B 2JA5D 2E9WC 4BBRD 1PW6A 1HIJA 3H3VE 2JA8D 2IL6A 4NI7A 3HOZD 3Q1SI 3QWRB 4IU8A 5TS9A 2B90A 3HOXD 5A2OA 3O7QA 3OG4A 1Y6ML 2O26A 4GRWA 1HWHA 2HYMB 1CNT1 1RFBA 1WU3I 1GNCA 1YKBA 4X51A 3S9DA 2Z3QA 4IKVA 1HWGA 4Q65A 5D22A 4UVMA 3SE3B 3UEZE 4DKFA 4GBZA 4YBQA 3L5WI 2Z3RA 4OH3A 4IKWA 1A22A 4BY7D 1M47A 1Y1VD 4DKCA 1KF9A 5D71A 4TPGA 1BBNA 1M4AA 1M48A 4QIQA 5D72A 4IKYA 1IRLA 2B5IA 4I77Z 5C65A 1PGRA 1Z7CA 2ILKA 4A3MD 1CN4C 1I1RB 4J05A 2LMSA 5L6YC 3HHCA 1D9CA 4U4WA 2CFPA 1BGDA 4LEPA 3PIWA 3EW3A 3IRHA 3G6DA 1J7VL 4J4LC 4JA3A 3WCYI 2D9QA 4A3FD 3DUHC 4D2DA 3NPZA 5IYBD 1HULA 3HOVD 1F6FA 3DI3A 2JA7D 1IJZA 1Y14A 4GBYA 2JA6D 1BGCA 3VA2A 3L5XA 5EQGA 4YQXA 4U4VA 2O27A 4IKXA 3QB1A 4ZWCA 4APSA 4D2BA 4TPHA 5FLMD 3NCBA 4IKZA 4CNIC 1ITMA 2B8ZA 1Y6NL 2H24A 1LQSL 5FUCA 1CD9A 4ZWBA 4PS4A 2O6IA 2V8NA 5IP7D 5IYDD 1BP3A 3SE4B 1PV6A 4ZYRA 1LK3A 1EKUA 2XUTA 2CFQA 4A3GD 2B91A 2D48A 4LRLA 4D2CA 4W6VA 1BUYA 1M4RA 1EMRA 3HHRA 4ZS7A 4YPGC 1M4CA 3D48P 1HZIA 3BPOA 2Q98A 2INTA 5A2NA 3D87A 4WRLB 3AYHA 5C44D 4JR9A 4Z5RD 4DKDA 2B8XA 3NCEA 3DI2A 3UF2A 3HOUD
chains in the Genus database with same CATH topology
5C4XD 2B90A 1V7NV 4NEJA 3HOXD 5E4EA 1BCNA 1J7VL 1HUWA 4J4LC 3WCYI 2D9QA 3OG4A 4A3FD 2LAGA 3DUHC 1Y6ML 3BPNA 1Y1WD 2O26A 5FHXA 3QT2C 4A3DD 1V7MV 3INKC 4A3CD 4GRWA 1HWHA 2HYMB 1P9MB 5C3ED 4BXXD 1WU3I 1CNT1 1RFBA 2Q14A 1PY2A 3NCFA 2C35A 1HULA 1Y6KL 3NPZA 5IYBD 1ITFA 1GNCA 1QVNA 1IL6A 1YKBA 4X51A 3S9DA 3HOVD 1F6FA 2Z3QA 4BY1D 4MHLA 4NN6A 1HWGA 3DI3A 3DLQI 3OG6A 1WCMD 2JA7D 3QAZA 1FYHA 1IJZA 4O6KA 3D85C 4A3BD 5D22A 1Y14A 3SE3B 3UEZE 2B8UA 2JA6D 1BGCA 3VA2A 1SCFA 2KZ1A 2B8YA 3BESL 1CYLA 1N1FA 3UF5A 3L5XA 4DKFA 2OQPA 4YQXA 1BGEA 1ETEA 1FG9A 3LB6A 2O27A 1RW5A 2GMFA 2Q7NB 4A3KD 4BBSD 1LKIA 1M4BA 4A3ID 1ITLA 5IYCD 2L3OA 3QB1A 3L5WI 2Z3RA 4NEMA 1ILKA 1AU1A 3FKID 1A7MA 5FLMD 1CSGA 1B5LA 3NCBA 4GS7A 3G9VB 4RS1A 1RCBA 4CNIC 3B5KA 1EERA 3EJJA 3QB7A 3I4ND 1ITMA 2B8ZA 1Y6NL 1HIKA 1A22A 2H24A 4BY7D 5KNHI 2L3YA 5LQBA 1LQSL 1M47A 1Y1VD 5FUCA 1CD9A 4DKCA 2R7ZD 1KF9A 4PS4A 2O6IA 4DOHA 5D71A 3PO3D 5C7XA 4A3ED 1GA3A 2PSMA 5IP7D 5IYDD 1BP3A 1D9GA 1BBNA 4A3JD 4YUEC 1F45B 1M49A 3SE4B 5IP9D 4EXPA 1LK3A 4A93D 1EKUA 1M4AA 1M48A 3H0GD 4A3GD 3IRHA 2B91A 4A3LD 1AXIA 2D48A 4O9HA 4LRLA 1PVHB 5D70A 5D72A 1BUYA 1M4RA 3UX9A 1EMRA 3HHRA 3HOYD 4ZF7A 4NN5A 4ZS7A 1IRLA 1IARA 3BPLA 2B5IA 4NN7A 2CYKA 3DGCL 1INRA 3PIVA 1EVSA 3N06A 1PGRA 4I77Z 4YPGC 3PO2D 4NKQC 2R92D 1M4CA 1Z7CA 2B63D 1NBPA 2ILKA 1VLKA 3D48P 4YDYI 1HZIA 4A3MD 3BPOA 4NI9A 1CN4C 3HMXB 1I1RB 4DKEA 2Q98A 1HGUA 2INTA 3TGXB 5D28B 4EXNA 3HOWD 2XQBA 1ITIA 2ERJD 1EXZA 2LMSA 3N0PA 3D87A 3NCCA 4FA8E 1ALUA 3MZGA 3OQ3A 3AYHA 4WRLB 5L6YC 3I4MD 2R93D 1Z92A 3HHCA 3LB6B 1D9CA 2E9WC 5C44D 2JA5D 4BBRD 2VUMD 1PW6A 1HIJA 3H3VE 2JA8D 2IL6A 1BGDA 4Z5RD 4NI7A 1RHGA 3HOZD 1IK0A 3PIWA 3Q1SI 2B8XA 3EW3A 1AX8A 3NCEA 3QWRB 4DKDA 3DI2A 1JLIA 5TS9A 3UF2A 3HOUD 3G6DA
chains in the Genus database with same CATH homology


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