4A3LD

Rna polymerase ii initial transcribing complex with a 7nt dna-rna hybrid and soaked with ampcpp
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
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 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; 4a3lD02
3FKID 4A3DD 5C44D 4A3LD 1Y1VD 4A3ED 3HOUD 2R7ZD 4A3BD 4A3GD 2JA5D 3HOVD 3HOZD 3HOYD 5FLMD 4A3MD 4A3FD 2R92D 3H3VE 4A3ID 4BBRD 5C3ED 2JA8D 3H0GD 1Y14A 5IYCD 4A3KD 4A3CD 4BBSD 2JA7D 3AYHA 2R93D 4BY1D 3I4ND 5C4XD 3PO3D 5IP9D 5IP7D 5IYDD 4A3JD 4BY7D 4BXXD 1Y1WD 2JA6D 3I4MD 1WCMD 3HOWD 5IYBD 3PO2D 3HOXD 4A93D 2B63D 2VUMD 2C35A
chains in the Genus database with same CATH superfamily
4YB9D 1EXZA 1CD9A 3HOZD 1Y6NL 4U4WA 1HWGA 1Z7CA 1I1RB 2E9WC 1LQSL 1D9CA 1HIKA 5IYDD 4GS7A 4NKQC 4WRLB 3BPNA 3QT2C 1BP3A 2B63D 3N06A 3O7PA 5C44D 5C7XA 2HYMB 4J4LC 4X51A 1RHGA 3SE3B 4GBZA 3H0GD 4A3KD 2INTA 4RS1A 1HWHA 5C4XD 1CSGA 1ITLA 5IP9D 1PW6A 1IRLA 1V7MV 4W6VA 4DKEA 1HGUA 4O9HA 1BUYA 3QAZA 3INKC 4YPGC 4UVMA 3LB6A 3MZGA 1PY2A 1QVNA 4JREA 2JA7D 5L6YC 3HHRA 1BGDA 4IU8A 4YUEC 4GC0A 4YBQA 1M4RA 1RCBA 3DUHC 2Z3RA 3EJJA 2Y5YA 3NCFA 5FUCA 4O6KA 4IKYA 3OG4A 1Y1VD 1BGEA 4XNJA 3WDOA 1GNCA 1SCFA 4JR9A 1D9GA 4NI7A 3S9DA 5EQIA 1HIJA 4LEPA 5IP7D 1J7VL 1B5LA 3DGCL 3WCYI 3SE4B 1FG9A 1EMRA 3UX9A 4A3DD 1FYHA 4ZS7A 2R7ZD 4D2BA 3HOVD 4TPHA 4NEMA 5TS9A 3PIVA 3DI3A 5D71A 3BESL 2GMFA 1P9MB 3DI2A 4D2DA 1HULA 4IKWA 1Z92A 2D9QA 4IKXA 5KNHI 2L3YA 4LRLA 4OAAA 2O26A 5FLMD 4Z5RD 4A3MD 1M49A 3L5WI 1KF9A 3D48P 1N1FA 1A7MA 1YKBA 1RFBA 4D2CA 4DKFA 5D28B 2B8YA 4GRWA 1PGRA 3QB1A 3FKID 3LB6B 3UEZE 5C65A 4DKDA 4A3FD 2B90A 1RW5A 5C3ED 2JA8D 4A3CD 1IJZA 2PSMA 4TPJA 1Y6ML 4A93D 1NBPA 2VUMD 3UF2A 3NCCA 1F45B 3HOUD 4A3ED 3D87A 5LQBA 1EVSA 4A3ID 4LDSA 2Z3QA 3I4ND 4BXXD 2L3OA 3G9VB 3BPOA 3O7QA 1BBNA 3EW3A 4CNIC 3QWRB 3VA2A 1M4CA 1PW4A 1ITMA 1CYLA 4MHLA 5EQHA 2XUTA 1ITFA 4BBSD 1BGCA 1WCMD 5E4EA 1A22A 4JA3A 1ETEA 4NN7A 3HOXD 2IL6A 2B8XA 2O27A 5GXBA 4A3LD 5D6KA 4YDYI 1LKIA 2JA5D 1HZIA 2Q98A 3H3VE 4DOHA 4Q65A 5A2OA 4GBYA 5D72A 1CNT1 2Q14A 2O6IA 2LAGA 4NEJA 4NN6A 4PYPA 2H24A 1F6FA 4A3BD 3UF5A 1BCNA 1INRA 3B5KA 1ALUA 2R92D 5D59A 3AYHA 2ERJD 1AU1A 2JA6D 1M48A 1IK0A 2B91A 1PV7A 3HMXB 4EXPA 4TPGA 2CFPA 5D70A 5EQGA 1Y14A 4U4TA 1CN4C 1M4BA 2R93D 4U4VA 4EXNA 2B8ZA 3PO3D 3NCEA 1EERA 3OG6A 1Y1WD 2ILKA 1PVHB 3HHCA 2V8NA 4APSA 4NN5A 4NI9A 4A3GD 2LMSA 1M4AA 2B5IA 5D58A 4ZF7A 1PV6A 3N0PA 5D22A 4ZWBA 3NCBA 5IYBD 2OQPA 3IRHA 1IL6A 1HUWA 3D85C 4I77Z 3DLQI 4ZYRA 1V7NV 1GA3A 2B8UA 1VLKA 3BPLA 2Q7NB 3PIWA 4QIQA 3I4MD 4YQXA 3QB7A 5A2NA 4OH3A 3HOYD 2CFQA 4IKZA 2KZ1A 4BY1D 3Q1SI 4ZW9A 2XQBA 1EKUA 1LK3A 1ILKA 4ZWCA 4A3JD 1IARA 3G6DA 3OQ3A 1M47A 2D48A 4IU9A 4FA8E 3NPZA 3TGXB 1AX8A 1ITIA 5FHXA 4BBRD 5IYCD 1WU3I 4PS4A 3L5XA 4BY7D 1JLIA 4J05A 3HOWD 3PO2D 2CYKA 1Y6KL 4IKVA 4DKCA 1AXIA 4XNIA 2C35A
chains in the Genus database with same CATH topology
3UX9A 4A3DD 1FYHA 1BBNA 3EW3A 1EXZA 4CNIC 3QWRB 4ZS7A 3VA2A 1CD9A 3HHCA 1M4CA 4NI9A 4NN5A 2R7ZD 4A3GD 3HOVD 3HOZD 2LMSA 1M4AA 1ITMA 1CYLA 1Y6NL 2B5IA 4NEMA 5TS9A 1HWGA 4MHLA 1Z7CA 3PIVA 1I1RB 4ZF7A 1ITFA 4BBSD 1BGCA 2E9WC 1LQSL 3N0PA 5D22A 3DI3A 1D9CA 1HIKA 3NCBA 5IYDD 1WCMD 4GS7A 4NKQC 4WRLB 5IYBD 5E4EA 3BPNA 5D71A 1A22A 3BESL 1ETEA 2GMFA 1BP3A 3QT2C 4NN7A 3HOXD 2OQPA 2IL6A 2B8XA 2B63D 3N06A 1P9MB 2O27A 3DI2A 3IRHA 5C44D 1IL6A 1HUWA 5C7XA 1HULA 4A3LD 1Z92A 2D9QA 2HYMB 4J4LC 4YDYI 5KNHI 1LKIA 2L3YA 3D85C 2JA5D 4LRLA 4X51A 1RHGA 4I77Z 2O26A 3SE3B 5FLMD 4Z5RD 4A3MD 1HZIA 2Q98A 1M49A 3DLQI 1V7NV 3H3VE 1GA3A 3L5WI 3H0GD 2B8UA 1KF9A 3D48P 4DOHA 4A3KD 1N1FA 2INTA 1A7MA 1YKBA 4RS1A 1RFBA 1HWHA 1VLKA 5C4XD 1CSGA 1ITLA 3BPLA 1PW6A 2Q7NB 4DKFA 3PIWA 5IP9D 5D28B 1IRLA 1V7MV 5D72A 3I4MD 1CNT1 2B8YA 2Q14A 4GRWA 1PGRA 2O6IA 4YQXA 3QB1A 3FKID 3LB6B 2LAGA 3QB7A 3UEZE 4DKEA 1HGUA 4O9HA 1BUYA 3QAZA 4NEJA 2H24A 3INKC 4NN6A 1F6FA 4A3BD 3UF5A 1BCNA 4YPGC 3LB6A 3HOYD 1INRA 3MZGA 4DKDA 1PY2A 3B5KA 4A3FD 1QVNA 1ALUA 2R92D 2B90A 1RW5A 5C3ED 2JA8D 4A3CD 2JA7D 5L6YC 2KZ1A 3HHRA 3AYHA 1BGDA 4BY1D 3Q1SI 1IJZA 2ERJD 1EKUA 2PSMA 2XQBA 4DKCA 1LK3A 1ILKA 4YUEC 4A3JD 1AU1A 1IARA 3G6DA 2JA6D 1M4RA 1RCBA 3DUHC 1M47A 2Z3RA 3OQ3A 3EJJA 1Y6ML 2D48A 4A93D 1NBPA 1M48A 2VUMD 3NCFA 1IK0A 2B91A 5FUCA 3HMXB 3NCCA 4O6KA 3UF2A 4EXPA 4FA8E 3NPZA 3OG4A 1F45B 1Y1VD 1BGEA 4A3ED 3HOUD 3D87A 5D70A 5LQBA 3TGXB 1AX8A 1GNCA 1SCFA 1D9GA 1EVSA 4A3ID 1ITIA 5FHXA 4BBRD 1Y14A 5IYCD 1CN4C 1M4BA 4NI7A 1WU3I 2Z3QA 3S9DA 2R93D 4PS4A 4EXNA 1HIJA 3L5XA 2B8ZA 3I4ND 3PO3D 5IP7D 3NCEA 1J7VL 1EERA 1JLIA 4BY7D 3OG6A 1Y1WD 2ILKA 1B5LA 3HOWD 4BXXD 3DGCL 3WCYI 3SE4B 2CYKA 3PO2D 2L3OA 1Y6KL 1FG9A 1EMRA 3G9VB 3BPOA 1PVHB 1AXIA 2C35A
chains in the Genus database with same CATH homology


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