4A3GD

Rna polymerase ii initial transcribing complex with a 2nt dna-rna hybrid
Total Genus 52
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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
52
sequence length
219
structure length
178
Chain Sequence
b'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 keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
molecule tags Transcription
total genus 52
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; 4a3gD02
5IP9D 1Y14A 4A3JD 2JA7D 1WCMD 2R7ZD 2B63D 1Y1WD 5C3ED 3AYHA 2JA6D 3HOWD 3HOYD 4A3ED 3HOZD 3HOVD 4A3DD 4BXXD 4A3LD 5IYBD 3HOXD 2VUMD 4BBSD 2R92D 5IP7D 5IYDD 5C4XD 4BY7D 4A3MD 5FLMD 4A3FD 4A3BD 5C44D 2C35A 3I4MD 3H0GD 2JA5D 4A3CD 4A93D 4A3ID 5IYCD 3FKID 1Y1VD 4A3GD 4A3KD 3I4ND 3PO2D 3H3VE 3HOUD 3PO3D 2R93D 4BBRD 4BY1D 2JA8D
chains in the Genus database with same CATH superfamily
3D85C 1Y1WD 3HOZD 1B5LA 1FG9A 3BPOA 4IKXA 1IL6A 4YUEC 2KZ1A 1GA3A 2B90A 4U4VA 3QT2C 1HGUA 2INTA 3N06A 1M4CA 4TPJA 1EXZA 3D48P 3NCCA 3SE4B 4ZWCA 1Z92A 5EQGA 1RFBA 1RCBA 4FA8E 3OQ3A 3B5KA 2ILKA 5D59A 3O7QA 3NCEA 3G6DA 4UVMA 1FYHA 3FKID 5A2OA 2D48A 5LQBA 4MHLA 1IJZA 4LDSA 2O26A 1ITFA 3OG6A 3UF2A 1HUWA 5D72A 1M47A 4U4TA 1ETEA 4W6VA 2L3OA 3PIVA 1I1RB 4A3FD 4XNIA 4LRLA 3D87A 2V8NA 2LMSA 4XNJA 5A2NA 1WU3I 4A3GD 3PO2D 4NKQC 4DKEA 1ITLA 4GRWA 4BY1D 1PW4A 4Z5RD 4A3JD 1WCMD 4PYPA 3G9VB 4IKYA 1HIKA 4IU8A 3PIWA 1EKUA 1V7MV 2XUTA 5IYCD 4NEMA 1LQSL 1PV7A 3LB6A 4LEPA 4OAAA 3UEZE 4NI9A 3L5XA 1AXIA 2OQPA 3LB6B 5IYBD 3SE3B 4A3BD 1CN4C 1BUYA 4NN6A 1CSGA 4GBZA 4IKWA 1A7MA 5E4EA 4O6KA 4D2BA 2B91A 2HYMB 5GXBA 1SCFA 2JA7D 3L5WI 2O6IA 4DKCA 4A3ED 2D9QA 3INKC 4BBSD 5IP7D 1BGEA 1D9CA 4BY7D 4X51A 4YDYI 4J05A 4IKVA 1M4AA 3O7PA 3BPNA 1EMRA 4NN5A 4QIQA 1P9MB 4TPGA 4WRLB 4PS4A 5C3ED 1PGRA 4RS1A 1QVNA 2JA6D 3HOYD 2GMFA 3HOVD 2VUMD 5C44D 3UF5A 1J7VL 4I77Z 2XQBA 3NCBA 1A22A 3QWRB 1PVHB 3S9DA 4APSA 2ERJD 2R7ZD 5FUCA 3Q1SI 2R92D 3TGXB 4ZF7A 3BESL 3HHRA 4ZYRA 2B5IA 3MZGA 1LKIA 4DOHA 3IRHA 1PY2A 3AYHA 3QB1A 3HOWD 1VLKA 3HOXD 3DI2A 4ZWBA 1ALUA 4A3MD 1V7NV 1Y6NL 1IRLA 1RW5A 3VA2A 3NPZA 4J4LC 4JA3A 2Z3QA 4IU9A 5C4XD 5EQHA 1M4BA 4NI7A 4OH3A 4NN7A 3EW3A 3WCYI 4TPHA 2O27A 4A3ID 5C65A 3HMXB 5D22A 2B8YA 4D2CA 5D70A 4GS7A 4BBRD 3OG4A 4EXNA 2IL6A 3UX9A 4GBYA 5D6KA 3NCFA 1F6FA 2B8XA 3WDOA 1NBPA 2B8UA 3DUHC 5KNHI 2PSMA 1IK0A 3HOUD 3PO3D 2R93D 1HZIA 2L3YA 4O9HA 1AU1A 5EQIA 5IYDD 3QAZA 5L6YC 1INRA 1PW6A 4Q65A 3I4MD 1LK3A 1BCNA 4JR9A 4A93D 1Y1VD 4YPGC 2E9WC 1PV6A 2Y5YA 1ILKA 4U4WA 5FHXA 3N0PA 1Y14A 4ZW9A 2Q14A 1D9GA 1IARA 1Z7CA 4BXXD 4JREA 3QB7A 4EXPA 3DI3A 1HWHA 2JA5D 4A3CD 4DKFA 4YBQA 4A3KD 4YQXA 2Q7NB 2JA8D 2LAGA 2CYKA 4D2DA 1KF9A 4A3DD 1EVSA 2CFQA 4DKDA 5FLMD 1RHGA 5D58A 4ZS7A 4NEJA 1M48A 4GC0A 5C7XA 1F45B 3H0GD 4CNIC 1BGDA 5D71A 2CFPA 1CNT1 3EJJA 5TS9A 5IP9D 2B8ZA 1AX8A 3DGCL 1BGCA 3DLQI 1HWGA 1ITMA 2C35A 1Y6ML 4IKZA 2H24A 1M49A 1EERA 3BPLA 1BBNA 1HIJA 1N1FA 3H3VE 1Y6KL 1CD9A 1ITIA 2B63D 1CYLA 1GNCA 4A3LD 1YKBA 1BP3A 5D28B 1M4RA 2Q98A 4YB9D 1JLIA 3I4ND 3HHCA 2Z3RA 1HULA
chains in the Genus database with same CATH topology
1Y14A 4NI9A 3L5XA 1AXIA 1LKIA 3D85C 2Q14A 4DOHA 1Y1WD 2OQPA 1PY2A 1D9GA 3AYHA 3IRHA 1IARA 3QB1A 3HOWD 3HOZD 1B5LA 1Z7CA 1VLKA 3LB6B 3DI2A 5IYBD 1ALUA 3HOXD 4BXXD 1FG9A 3SE3B 3BPOA 4A3MD 1IL6A 3QB7A 1V7NV 1Y6NL 1IRLA 4EXPA 4A3BD 1RW5A 3DI3A 4YUEC 2KZ1A 1GA3A 1CN4C 1HWHA 3VA2A 2JA5D 2B90A 4A3CD 4DKFA 1BUYA 4NN6A 1CSGA 3QT2C 1A7MA 5E4EA 3NPZA 1HGUA 2INTA 4J4LC 4O6KA 4A3KD 3N06A 4YQXA 1M4CA 2B91A 1EXZA 2Q7NB 3D48P 2HYMB 3NCCA 2JA8D 1SCFA 2Z3QA 3SE4B 2JA7D 2LAGA 2CYKA 3L5WI 2O6IA 4DKCA 1Z92A 1KF9A 4A3ED 2D9QA 4A3DD 1EVSA 3INKC 1RFBA 4BBSD 5IP7D 1BGEA 1D9CA 5C4XD 4BY7D 1RCBA 4FA8E 3OQ3A 4DKDA 4X51A 1M4BA 1RHGA 3B5KA 4YDYI 5FLMD 2ILKA 4NI7A 4NN7A 1M4AA 1M48A 3G6DA 3NCEA 4NEJA 3BPNA 1EMRA 1F45B 3EW3A 3H0GD 3WCYI 4CNIC 5C7XA 1FYHA 1BGDA 2O27A 5D71A 3FKID 4A3ID 4NN5A 3HMXB 5D22A 2D48A 1CNT1 1P9MB 2B8YA 3EJJA 5D70A 5LQBA 4GS7A 4BBRD 4MHLA 3OG4A 1IJZA 5TS9A 5IP9D 4EXNA 2IL6A 4WRLB 4PS4A 2B8ZA 2O26A 1AX8A 3DGCL 3UX9A 1PGRA 3OG6A 4RS1A 3UF2A 1QVNA 5C3ED 2JA6D 1ITFA 3HOYD 2GMFA 1BGCA 1HUWA 5D72A 1M47A 3HOVD 2VUMD 3NCFA 1ETEA 1F6FA 2L3OA 3PIVA 3DLQI 1HWGA 1I1RB 4A3FD 2B8XA 3PO2D 5C44D 1ITMA 1NBPA 1Y6ML 2C35A 3D87A 2H24A 4LRLA 1M49A 1EERA 2LMSA 3UF5A 1J7VL 4I77Z 1IK0A 2B8UA 1WU3I 3DUHC 4A3GD 2XQBA 3PO3D 3NCBA 3BPLA 2PSMA 5KNHI 1A22A 1BBNA 1HIJA 1N1FA 3QWRB 1ITLA 4GRWA 4NKQC 4DKEA 1PVHB 3S9DA 1HZIA 4BY1D 2R93D 4Z5RD 1Y6KL 1CD9A 4A3JD 2ERJD 1ITIA 1WCMD 2R7ZD 2B63D 5FUCA 1CYLA 3G9VB 2L3YA 4O9HA 3Q1SI 1GNCA 4A3LD 1AU1A 1YKBA 3HOUD 2R92D 5IYDD 3TGXB 1HIKA 4ZF7A 3QAZA 5L6YC 3H3VE 3BESL 3PIWA 1BP3A 1INRA 1PW6A 3HHRA 1EKUA 3UEZE 3I4MD 1V7MV 1LK3A 5D28B 1BCNA 1M4RA 4A93D 5IYCD 1Y1VD 2Q98A 4ZS7A 4YPGC 4NEMA 1LQSL 1JLIA 2B5IA 2E9WC 3I4ND 3HHCA 1ILKA 3MZGA 3LB6A 2Z3RA 5FHXA 1HULA 3N0PA
chains in the Genus database with same CATH homology


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