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


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