4A3MD

Rna polymerase ii initial transcribing complex with a 4nt dna-rna hybrid and soaked with ampcpp
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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publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
molecule tags Transcription
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; 4a3mD02
3HOVD 5IYCD 3I4ND 3FKID 4BY7D 4BBRD 3HOXD 4BY1D 5C4XD 3AYHA 4BXXD 4A3BD 4BBSD 1WCMD 3PO3D 3H0GD 3PO2D 4A3FD 3HOUD 2R7ZD 3HOYD 2C35A 4A3JD 5IP7D 4A3ED 2R93D 3HOZD 2JA8D 1Y1VD 2JA7D 2R92D 3H3VE 4A3ID 1Y14A 4A3LD 5IP9D 4A3MD 4A3GD 5IYBD 4A3DD 5C44D 3I4MD 4A3CD 3HOWD 4A3KD 2VUMD 5IYDD 2B63D 1Y1WD 2JA5D 5FLMD 2JA6D 5C3ED 4A93D
chains in the Genus database with same CATH superfamily
1INRA 4BY7D 4NI7A 1EXZA 1BGDA 3HOYD 1HGUA 1IARA 3WCYI 3SE3B 5D72A 4A3LD 4A3GD 4D2BA 4I77Z 1HWGA 2B63D 5TS9A 4YQXA 4O6KA 4QIQA 1GNCA 2L3YA 2R7ZD 1M47A 4YUEC 2XUTA 3NCCA 1I1RB 4NEMA 1IJZA 1PVHB 1JLIA 1Y6ML 5IYDD 4DKFA 4GRWA 2XQBA 1KF9A 3G6DA 4LDSA 3I4ND 4OH3A 4FA8E 4O9HA 2B5IA 2OQPA 2IL6A 3IRHA 4XNIA 4WRLB 4JA3A 4PS4A 3D48P 3DI2A 1CN4C 5IP7D 1HULA 3QAZA 2R92D 2O6IA 4DKDA 3BPNA 3HOWD 5L6YC 1IK0A 3MZGA 1HIJA 4EXPA 1LQSL 5FLMD 5C3ED 5LQBA 1GA3A 4ZF7A 2CFPA 4BBRD 1AU1A 1EVSA 3EJJA 3LB6A 3NCBA 5D22A 3QT2C 3DI3A 4LEPA 5EQGA 2D9QA 3H3VE 2H24A 2ERJD 1PV6A 4GBZA 4NN7A 3D85C 1Y6KL 5IYCD 1BGEA 3HHRA 5FHXA 4ZYRA 1WU3I 3DLQI 1M4AA 4NKQC 1FYHA 3EW3A 1IRLA 4D2CA 3BESL 4MHLA 3OG6A 4IU8A 3NCEA 5D6KA 1HZIA 1BBNA 3PO3D 3UF5A 1LKIA 2HYMB 3N06A 4A3JD 3N0PA 4A3ED 3PIWA 1Z7CA 1CNT1 2B8UA 2JA8D 4PYPA 1Y1VD 5A2OA 2LMSA 4NN6A 4CNIC 1Y1WD 3TGXB 3UF2A 1P9MB 4Z5RD 4LRLA 3PO2D 4IU9A 5E4EA 3LB6B 5D58A 5A2NA 4U4TA 1SCFA 4D2DA 1FG9A 4JR9A 1ITLA 1IL6A 4BY1D 1HIKA 1CD9A 1RHGA 3S9DA 3D87A 5D28B 2L3OA 4IKYA 3VA2A 2CFQA 3PIVA 3DUHC 1CYLA 3OQ3A 4XNJA 4YDYI 4OAAA 5EQHA 5C4XD 1QVNA 1WCMD 2B8ZA 3G9VB 4BBSD 3O7QA 4EXNA 1M48A 4APSA 4YBQA 5GXBA 4IKWA 4IKVA 1PW4A 2B90A 1BCNA 3SE4B 1ALUA 4YB9D 4RS1A 2D48A 4ZW9A 3UX9A 4DKEA 1PV7A 3FKID 3AYHA 5C65A 2Q14A 3DGCL 4J05A 3BPOA 3NCFA 3L5XA 3HMXB 4A3CD 1M4RA 4Q65A 5C7XA 1J7VL 2ILKA 1LK3A 1D9GA 2R93D 1YKBA 2B91A 1B5LA 1AXIA 1D9CA 1BUYA 1RCBA 5IP9D 4A3MD 4ZS7A 4W6VA 2LAGA 4JREA 1PW6A 5D59A 5D70A 1BP3A 1RW5A 3NPZA 3L5WI 3WDOA 5EQIA 4TPJA 2V8NA 4A3ID 1M49A 4NI9A 4TPHA 4A3DD 4A3KD 4IKXA 1RFBA 1HUWA 1ETEA 2JA5D 1F45B 4A93D 5D71A 1PY2A 1V7NV 2GMFA 4A3FD 4ZWCA 4U4WA 4U4VA 1AX8A 1EMRA 1F6FA 1A22A 3QB7A 5KNHI 4NEJA 4DKCA 4GC0A 4YPGC 2Q98A 5C44D 3I4MD 4ZWBA 2B8YA 2E9WC 3HOVD 1ILKA 3HOXD 4BXXD 3HHCA 3H0GD 3OG4A 3HOUD 2PSMA 2KZ1A 3Q1SI 3HOZD 1CSGA 2JA7D 1Z92A 3QWRB 1BGCA 2VUMD 3INKC 4GS7A 4IKZA 1ITFA 1Y6NL 1HWHA 1M4BA 1N1FA 1ITIA 2O26A 2O27A 5FUCA 1EERA 4NN5A 4X51A 3O7PA 5IYBD 3BPLA 1NBPA 2JA6D 2Y5YA 4DOHA 2Z3RA 2B8XA 4TPGA 4A3BD 3QB1A 1M4CA 2INTA 1V7MV 2C35A 3UEZE 1ITMA 4UVMA 2CYKA 4J4LC 1PGRA 1A7MA 1VLKA 2Z3QA 2Q7NB 1Y14A 3B5KA 1EKUA 4GBYA
chains in the Genus database with same CATH topology
1INRA 4YDYI 1BGEA 1PY2A 3HHRA 5D71A 5FHXA 1V7NV 5IYCD 4BY7D 5C4XD 2GMFA 3DUHC 4NI7A 1EXZA 1QVNA 1WCMD 2B8ZA 3G9VB 4EXNA 1WU3I 1BGDA 3DLQI 1M48A 1M4AA 4A3FD 3HOYD 4NKQC 1AX8A 1EMRA 1F6FA 1HGUA 1FYHA 1A22A 3QB7A 1IARA 3EW3A 1IRLA 5KNHI 4NEJA 4DKCA 3WCYI 2B90A 3SE3B 4YPGC 5D72A 4A3LD 1BCNA 3SE4B 2Q98A 4A3GD 1ALUA 5C44D 3I4MD 3BESL 4I77Z 4MHLA 4RS1A 2D48A 1HWGA 3UX9A 4DKEA 2B63D 5TS9A 4YQXA 3OG6A 2B8YA 3NCEA 4O6KA 1HZIA 2E9WC 3HOVD 1BBNA 3FKID 1ILKA 3HOXD 1CYLA 3AYHA 4BXXD 3PO3D 3HHCA 3UF5A 2Q14A 1GNCA 1LKIA 3H0GD 2L3YA 3OG4A 3DGCL 4A93D 3HOUD 2R7ZD 2PSMA 1M47A 2HYMB 3N06A 3N0PA 4YUEC 4A3JD 3BPOA 3NCFA 2KZ1A 1I1RB 3NCCA 3Q1SI 3PIWA 4A3ED 3HOZD 1Z7CA 1CNT1 2B8UA 4NEMA 2JA8D 1IJZA 1CSGA 1PVHB 1Y1VD 1Z92A 2JA7D 1JLIA 1Y6ML 3QWRB 2LMSA 3L5XA 3HMXB 4NN6A 4CNIC 1BGCA 4A3CD 1M4RA 2VUMD 5IYDD 3INKC 1Y1WD 3TGXB 4DKFA 4GRWA 3UF2A 1P9MB 4GS7A 2XQBA 1KF9A 3G6DA 4Z5RD 5C7XA 3I4ND 1J7VL 2ILKA 4FA8E 4O9HA 2B5IA 2OQPA 1LK3A 2IL6A 4LRLA 3IRHA 1ITFA 4WRLB 1Y6NL 3PO2D 1D9GA 4PS4A 3D48P 1HWHA 3DI2A 1CN4C 1N1FA 1M4BA 5IP7D 1HULA 1YKBA 5E4EA 2O26A 2O27A 2R93D 2B91A 1ITIA 3LB6B 5FUCA 1B5LA 3QAZA 1AXIA 1D9CA 1EERA 2R92D 2O6IA 4NN5A 1BUYA 1RCBA 1SCFA 4X51A 4DKDA 3BPNA 5IP9D 5IYBD 4A3MD 3BPLA 4ZS7A 3HOWD 5L6YC 1IK0A 1FG9A 3MZGA 1HIJA 1NBPA 4EXPA 1LQSL 1ITLA 2LAGA 5FLMD 2JA6D 5C3ED 5LQBA 1GA3A 4ZF7A 1PW6A 1IL6A 4DOHA 5D70A 4BBRD 2Z3RA 1BP3A 4BY1D 2B8XA 4A3BD 1AU1A 1EVSA 3QB1A 1M4CA 2INTA 1RW5A 1HIKA 1V7MV 1CD9A 3EJJA 2C35A 3LB6A 1ITMA 3L5WI 3NCBA 3NPZA 5D22A 3UEZE 3QT2C 1RHGA 2CYKA 4BBSD 4J4LC 1PGRA 3DI3A 1A7MA 1VLKA 2Z3QA 2D9QA 3H3VE 2Q7NB 3S9DA 1Y14A 4A3ID 3D87A 1M49A 3B5KA 1EKUA 4NI9A 4A3DD 5D28B 2H24A 2ERJD 4A3KD 1RFBA 2L3OA 1HUWA 1ETEA 4NN7A 3VA2A 3D85C 2JA5D 3PIVA 1Y6KL 1F45B 3OQ3A
chains in the Genus database with same CATH homology


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