3PO3D

Arrested rna polymerase ii reactivation intermediate
Total Genus 53

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
53
sequence length
218
structure length
177
Chain Sequence
STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

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
EMPTYTIV4 (31-34)TI1 (30-33)TIV3 (25-28)S2 (44-46)TI2 (39-42)S1 (36-38)TIV6 (73-76)AH2 (120-133)AH4 (157-170)TIV7 (135-138)AH3 (139-150)TVIII2 (152-155)AH5 (174-182)O1 (118-120)AH1 (54-73)TIV5 (51-54)Updating...
connected with : NaN
molecule tags Transferase/dna/rna
source organism Saccharomyces cerevisiae
publication title Structural basis of RNA polymerase II backtracking, arrest and reactivation.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 53
structure length 177
sequence length 218
ec nomenclature
pdb deposition date 2010-11-21

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; 3po3D02
3I4MD 3HOWD 4A3DD 3HOXD 5FLMD 3HOZD 5C44D 2JA8D 4BXXD 2VUMD 1Y1WD 3PO2D 5IP7D 4A93D 2R93D 4A3FD 4A3CD 3PO3D 4BY7D 5C4XD 4A3ID 3HOYD 5IYBD 4A3ED 2JA6D 3I4ND 4BBSD 3H3VE 4BY1D 3HOVD 4A3LD 2B63D 1WCMD 2JA7D 4A3KD 4A3MD 2JA5D 4A3GD 2R7ZD 5IP9D 1Y1VD 5IYDD 3FKID 3H0GD 2R92D 1Y14A 3AYHA 4A3JD 3HOUD 4BBRD 4A3BD 5C3ED 5IYCD 2C35A
chains in the Genus database with same CATH superfamily
1GNCA 1ALUA 2INTA 1IARA 4DKFA 2L3YA 5D72A 3HHCA 4ZW9A 2XUTA 1PGRA 4IKZA 3LB6A 3BPOA 3O7PA 4NN5A 3G9VB 4GBZA 3SE4B 4D2DA 1RW5A 1ITFA 1HZIA 5IP9D 3FKID 4JA3A 5L6YC 1PV6A 2B91A 4I77Z 4NI7A 3B5KA 4W6VA 5D71A 1QVNA 1KF9A 2O6IA 1IK0A 3QAZA 4A3ID 5IYBD 4LEPA 4OAAA 3OG6A 1RFBA 4U4TA 2JA5D 1A22A 4NEJA 1F45B 1ITLA 3DI2A 4BBRD 1A7MA 2C35A 3NCCA 3HOWD 2ERJD 1Y6NL 3L5WI 4A3CD 1D9GA 2B8ZA 4YPGC 4QIQA 1JLIA 4LDSA 1CSGA 1EXZA 1HIKA 1WCMD 4APSA 2IL6A 3DUHC 1RCBA 3S9DA 2B90A 1HIJA 1N1FA 1EMRA 4PYPA 4OH3A 3HHRA 1M47A 4IU8A 4RS1A 4J05A 3QT2C 3DGCL 4JR9A 3PO2D 3PO3D 2PSMA 4IKWA 3UEZE 2V8NA 2JA6D 2Z3RA 2B63D 5A2NA 2B8XA 4IKYA 4GC0A 5GXBA 1BP3A 3UX9A 2Z3QA 2OQPA 4NEMA 2LAGA 2D9QA 1BGEA 4GBYA 2B8UA 2H24A 3IRHA 3TGXB 4JREA 1BGCA 3D48P 4NKQC 5FHXA 1ILKA 3AYHA 4X51A 1PVHB 3O7QA 2VUMD 1CN4C 3OG4A 1HUWA 3NPZA 1Y1WD 1Y6KL 1BBNA 1M4RA 1M49A 2O26A 4D2CA 4GS7A 4BY1D 1CD9A 3INKC 1I1RB 1PV7A 5D58A 1V7MV 1V7NV 3HOXD 4Q65A 4BY7D 3L5XA 4GRWA 4TPGA 1FG9A 4Z5RD 3HMXB 2KZ1A 2B8YA 4A3GD 4IU9A 3QB1A 4ZS7A 4YBQA 4XNJA 1F6FA 3WDOA 4A3DD 4LRLA 4UVMA 5IP7D 1BGDA 3N06A 5C7XA 4J4LC 1YKBA 4YQXA 5A2OA 1HWGA 1HWHA 1ITIA 1INRA 2R7ZD 3DLQI 4PS4A 1GA3A 1EERA 2E9WC 4DKEA 4FA8E 2CFPA 4WRLB 4ZWCA 4A3FD 4ZYRA 5FUCA 3PIVA 3EJJA 5D22A 4U4VA 1VLKA 4A3MD 1B5LA 2R92D 1Y14A 1D9CA 5TS9A 2LMSA 1P9MB 5D59A 4ZWBA 3OQ3A 3D87A 5D6KA 5EQGA 1SCFA 3BPNA 2JA7D 3Q1SI 2L3OA 3HOUD 4A3BD 4DKCA 3NCFA 5LQBA 1AU1A 2HYMB 3D85C 5FLMD 1Z92A 2D48A 1LQSL 4DOHA 2Y5YA 3G6DA 1HGUA 1ETEA 1WU3I 1RHGA 3HOYD 4A3ED 1LKIA 3I4ND 3H3VE 2XQBA 1BCNA 2ILKA 3UF5A 4A3LD 2GMFA 3WCYI 1PW4A 4A3JD 3NCEA 1BUYA 5IYCD 4NN6A 4MHLA 1Y6ML 5C44D 1CNT1 5E4EA 3PIWA 5EQHA 4YB9D 4BBSD 4D2BA 5D28B 4EXNA 4NN7A 1NBPA 5KNHI 1AX8A 3DI3A 4EXPA 1IL6A 2CFQA 1PY2A 5C4XD 1M4AA 1M4CA 4A3KD 1M48A 2Q98A 3QB7A 3BPLA 3LB6B 4O6KA 2O27A 1M4BA 4TPJA 4IKXA 4XNIA 4YDYI 1IJZA 3HOVD 5IYDD 1ITMA 3VA2A 1EVSA 2CYKA 4IKVA 5C3ED 3EW3A 2Q14A 2JA8D 1HULA 4BXXD 5C65A 2R93D 1EKUA 3MZGA 5D70A 4ZF7A 4NI9A 1FYHA 1J7VL 1LK3A 1Y1VD 3NCBA 1AXIA 1PW6A 3UF2A 3I4MD 3QWRB 3HOZD 5EQIA 3BESL 4A93D 2Q7NB 4DKDA 3N0PA 1Z7CA 4TPHA 4O9HA 4CNIC 1IRLA 1CYLA 3H0GD 2B5IA 3SE3B 4YUEC 4U4WA
chains in the Genus database with same CATH topology
1AX8A 4PS4A 1GA3A 1GNCA 1EERA 2E9WC 2OQPA 1ALUA 2INTA 3DI3A 4DKEA 4NEMA 1IARA 2LAGA 4EXPA 4FA8E 1IL6A 4WRLB 4DKFA 2L3YA 2D9QA 1BGEA 1PY2A 5D72A 4A3FD 3HHCA 5C4XD 5FUCA 1PGRA 2B8UA 2H24A 3BPOA 3EJJA 3IRHA 3LB6A 3PIVA 5D22A 4NN5A 1M4AA 3G9VB 3TGXB 1M4CA 3SE4B 1VLKA 1RW5A 4A3KD 1BGCA 4A3MD 1ITFA 1HZIA 5IP9D 3D48P 3FKID 1B5LA 1M48A 4NKQC 5FHXA 5L6YC 1ILKA 2R92D 2Q98A 1Y14A 3AYHA 4X51A 3QB7A 1PVHB 3BPLA 2B91A 4I77Z 4NI7A 3B5KA 1D9CA 5TS9A 2LMSA 1P9MB 1QVNA 3LB6B 5D71A 4O6KA 2O27A 2VUMD 1CN4C 1KF9A 3OG4A 1HUWA 1M4BA 3NPZA 1Y1WD 1Y6KL 1BBNA 2O6IA 1IK0A 1M4RA 1M49A 3QAZA 3OQ3A 2O26A 3D87A 4A3ID 5IYBD 4YDYI 1IJZA 4GS7A 3OG6A 4BY1D 1SCFA 3BPNA 1CD9A 1RFBA 3HOVD 3INKC 2JA7D 3Q1SI 2JA5D 1A22A 1I1RB 4NEJA 1ITMA 1F45B 5IYDD 3VA2A 2L3OA 1ITLA 3HOUD 1EVSA 3DI2A 4BBRD 4DKCA 4A3BD 1A7MA 1V7MV 2CYKA 3NCFA 1V7NV 5LQBA 5C3ED 2C35A 1AU1A 3EW3A 2HYMB 3NCCA 2Q14A 3D85C 3HOWD 3HOXD 2ERJD 5FLMD 1Z92A 1HULA 2D48A 2JA8D 4BXXD 1LQSL 4DOHA 3G6DA 1HGUA 1ETEA 1WU3I 2R93D 1Y6NL 1RHGA 3L5WI 4A3CD 1D9GA 1EKUA 4BY7D 3L5XA 4GRWA 2B8ZA 4YPGC 3HOYD 3MZGA 1LKIA 4A3ED 3I4ND 3H3VE 1FG9A 2XQBA 4Z5RD 1BCNA 1JLIA 3HMXB 2ILKA 3UF5A 5D70A 1CSGA 4ZF7A 1EXZA 1HIKA 2B8YA 1WCMD 2KZ1A 4A3LD 2IL6A 1FYHA 2GMFA 1J7VL 1LK3A 3DUHC 1Y1VD 3QB1A 4ZS7A 3WCYI 4NI9A 4A3GD 1RCBA 3NCBA 1AXIA 1PW6A 3S9DA 2B90A 1HIJA 1N1FA 4A3JD 1EMRA 3UF2A 3NCEA 1F6FA 1BUYA 5IYCD 4NN6A 3HHRA 4MHLA 1M47A 3I4MD 4A3DD 4RS1A 1Y6ML 3QWRB 3HOZD 3QT2C 5C44D 3BESL 4LRLA 1CNT1 3DGCL 5E4EA 3PIWA 3PO2D 5IP7D 4A93D 2Q7NB 1BGDA 2PSMA 3PO3D 3N06A 5C7XA 3UEZE 4J4LC 4BBSD 1YKBA 2JA6D 4DKDA 5D28B 3N0PA 4YQXA 4EXNA 1HWGA 1HWHA 2Z3RA 4NN7A 2B63D 1Z7CA 4O9HA 1ITIA 4CNIC 1IRLA 1INRA 2R7ZD 2B8XA 1CYLA 3DLQI 3H0GD 2B5IA 1BP3A 1NBPA 3UX9A 5KNHI 3SE3B 4YUEC 2Z3QA
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

Application loaded.