3LWPB

Structure of h/aca rnp bound to a substrate rna containing 5brdu
Total Genus 7
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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
7
sequence length
53
structure length
53
Chain Sequence
FRIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI
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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 Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study.
pubmed doi rcsb
molecule tags Isomerase/rna binding protein/rna
source organism Pyrococcus furiosus
molecule keywords Pseudouridine synthase Cbf5
total genus 7
structure length 53
sequence length 53
ec nomenclature
pdb deposition date 2010-02-24

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
B PF04135 Nop10p Nucleolar RNA-binding protein, Nop10p family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.20.28.40 Mainly Beta Single Sheet Rubrerythrin, domain 2 H/ACA ribonucleoprotein complex, subunit Nop10 3lwpB00
2APOB 3HJYB 3LWVB 2RFKB 3HAXC 3HJWB 3LWOB 3LWRB 2HVYC 2AQCA 3MQKB 2EY4E 3LWQB 3LWPB 2AUSB
chains in the Genus database with same CATH superfamily
1B2OA 4K9FA 5M3ML 1WCML 2AQCA 5C4XL 3GTJL 3LPEB 1RDVA 3RZTA 4C3HL 1FHHA 4AHZA 1RDGA 3KYUA 1IRNA 2JA5L 4BXXL 3LNLA 4JADA 1B71A 4JAFA 4A3DL 2RFKB 1IW7D 2R7ZL 5AN9H 2APOB 4B8CD 2HVYC 3I4NL 5MF6A 2NVTL 1VCXA 3ZG6A 3J7Z1 4WFN1 3KYXA 4LHLA 2CKAA 1LKMA 4AYBP 2JA8L 5M5XL 1Z92B 1TWAL 4A3ML 4A93L 3M4OL 2KN9A 3LWVB 1BQ9A 4BBSL 3M3YL 1IU5A 3HOVL 1H7VA 3S1NL 4AR5A 4TVMA 5K2ME 3HOUL 1SFOL 3MPSA 3GTML 2H12A 4BBRL 4ZN3B 3LWPB 3JR7A 1RB9A 2NYDA 1PFVA 3H99A 5MFPA 2NVXL 3H0GL 4POFA 2ZIXA 3KYYA 2M4YA 4AR6A 2XJUA 2EY4E 4AI0A 3H9CA 4ME3A 1BE7A 3CQZL 2Z3RB 2PVXA 3S16L 5C3EL 1NXEA 2PPTA 3QVDA 5H1Sc 2XJRA 3GTKL 1SMWA 1WJVA 2HR5A 4QIWP 1E8JA 4G6BA 5M3FL 5AI3A 3GTPL 1S30A 3KYVA 3MSUA 2J9UB 4A3GL 1ZRPA 1RYTA 2XJQA 4JAEA 3FKIL 2LCQA 1TWFL 1VZIA 4TPUA 1LKOA 2PYAA 1T9QA 1RWDA 2PVEA 3SS2A 8RXNA 2NVYL 5JVH1 4GS7D 1S2ZA 1BRFA 1R0HA 4XGHA 3NFPI 3RZOL 2C6BA 3H9BA 3PIO1 1BFYA 1QYBA 1YK5A 3GTGL 1OWBA 2XJSA 1YK4A 2PMZP 3HJYB 1T9PA 5FJ8L 5GAGc 2CKCA 1P7PA 3S2DL 2QL0A 2M6OA 2JA7L 1IU6A 3S15L 3GTLL 1DVBA 2XJTA 3VPBE 2E2JL 5M5WL 2B63L 1SMMA 4YWLA 3I4ML 1B2JA 4POGA 4C3JL 3PO2L 1F4LA 3HOWL 6RXNA 2A69D 3B0AB 3MQKB 2KKDA 4BY7L 4XXBB 4LHNA 3LWOB 3PKJA 1CADA 1VZHA 3S2HL 4BY1L 4AI3A 4X6AL 3PL5A 1LTLA 3PKIA 4E6YA 2M6PA 4RXNA 4A3IL 5C44L 1RYQA 4U671 1ODHA 1FHMA 1Y1VL 5IYBL 2JI2A 5GAEc 2NVQL 3HAXC 5GAHc 3HJWB 4JAGA 2A6ED 1JYBA 3HKZP 2K2DA 5MFZA 3HOZL 2VUML 3HOYL 5DM61 3WWNB 3PIP1 3K7AL 1C09A 3GTQL 5IYDL 2E2IL 2WAQP 2JI1A 5EIOC 5JVG1 4A3BL 2ERJA 3PZAA 2A68D 1Y1WL 3A44A 3RYGA 2O5JD 5DM71 2B5ID 2M4VA 4A3JL 2Z3QB 5IY0A 4AHXA 3B08B 3QQCE 3KYWA 3J7Y1 3S1RL 5IP9L 1PFUA 1YUXA 5M5YL 5GADc 2ERSA 5MLC3 3S1QL 3LWQB 3K35A 5C4JL 4ZN1B 3FDJA 4A3EL 4AI1A 1SMUA 2WB1P 1K83L 2V0FA 1IROA 1LKPA 2Y0SP 2XJVA 4AR4A 1QCVA 1TWCL 3IU3I 3RZ6A 1R0IA 5MGNA 1OWCA 2GMGA 1PFWA 1I6HL 3P2AA 3S1ML 5RXNA 3H3VM 1I50L 1R0JA 4A3CL 2PSMC 1I3QL 1VZGA 3S17L 1DX8A 2R93L 2JA6L 1PFYA 5FLML 3PO3L 3H97A 4C3IL 2VL6A 3HOXL 2R92L 3PWFA 1PZXA 1B13A 3S14L 4YWMA 1YUZA 2XJPA 4AHYA 4A3FL 2C6AA 2MS3A 4Y7NL 1NNQA 4Y52L 2JI3A 2A6HD 2AUSB 1R0FA 1TWGL 1CAAA 5IYCL 2BE5D 1TWHL 4C2M1 4AR3A 3GTOL 3WWLA 2V3BB 1R9TL 1T9OA 1R0GA 4V196 2V0EA 4A3LL 5IP7L 1QQTA 4A3KL 3RZDL 1NXGA 2YU9L 2DSXA 3P8BA 2AYJA 4UY81 4AI2A 2RDVA 1S24A 4AHWA 1YV1A 1BQ8A 7RXNA 5EINC 2L0ZA 2E2HL 2CR8A 3LWRB 5AI2A
chains in the Genus database with same CATH topology
2APOB 3HJYB 3LWVB 2RFKB 3HAXC 3HJWB 3LWOB 3LWRB 2HVYC 2AQCA 3MQKB 2EY4E 3LWQB 3LWPB 2AUSB
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2APO B;  3HJY B;  3LWV B;  2RFK B;  3HAX C;  3HJW B;  3LWO B;  3LWR B;  2HVY C;  2AQC A;  3MQK B;  2EY4 E;  3LWQ B;  3LWP B;  2AUS B; 
#chains in the Genus database with same CATH topology
 1B2O A;  4K9F A;  5M3M L;  1WCM L;  2AQC A;  5C4X L;  3GTJ L;  3LPE B;  1RDV A;  3RZT A;  4C3H L;  1FHH A;  4AHZ A;  1RDG A;  3KYU A;  1IRN A;  2JA5 L;  4BXX L;  3LNL A;  4JAD A;  1B71 A;  4JAF A;  4A3D L;  2RFK B;  1IW7 D;  2R7Z L;  5AN9 H;  2APO B;  4B8C D;  2HVY C;  3I4N L;  5MF6 A;  2NVT L;  1VCX A;  3ZG6 A;  3J7Z 1;  4WFN 1;  3KYX A;  4LHL A;  2CKA A;  1LKM A;  4AYB P;  2JA8 L;  5M5X L;  1Z92 B;  1TWA L;  4A3M L;  4A93 L;  3M4O L;  2KN9 A;  3LWV B;  1BQ9 A;  4BBS L;  3M3Y L;  1IU5 A;  3HOV L;  1H7V A;  3S1N L;  4AR5 A;  4TVM A;  5K2M E;  3HOU L;  1SFO L;  3MPS A;  3GTM L;  2H12 A;  4BBR L;  4ZN3 B;  3LWP B;  3JR7 A;  1RB9 A;  2NYD A;  1PFV A;  3H99 A;  5MFP A;  2NVX L;  3H0G L;  4POF A;  2ZIX A;  3KYY A;  2M4Y A;  4AR6 A;  2XJU A;  2EY4 E;  4AI0 A;  3H9C A;  4ME3 A;  1BE7 A;  3CQZ L;  2Z3R B;  2PVX A;  3S16 L;  5C3E L;  1NXE A;  2PPT A;  3QVD A;  5H1S c;  2XJR A;  3GTK L;  1SMW A;  1WJV A;  2HR5 A;  4QIW P;  1E8J A;  4G6B A;  5M3F L;  5AI3 A;  3GTP L;  1S30 A;  3KYV A;  3MSU A;  2J9U B;  4A3G L;  1ZRP A;  1RYT A;  2XJQ A;  4JAE A;  3FKI L;  2LCQ A;  1TWF L;  1VZI A;  4TPU A;  1LKO A;  2PYA A;  1T9Q A;  1RWD A;  2PVE A;  3SS2 A;  8RXN A;  2NVY L;  5JVH 1;  4GS7 D;  1S2Z A;  1BRF A;  1R0H A;  4XGH A;  3NFP I;  3RZO L;  2C6B A;  3H9B A;  3PIO 1;  1BFY A;  1QYB A;  1YK5 A;  3GTG L;  1OWB A;  2XJS A;  1YK4 A;  2PMZ P;  3HJY B;  1T9P A;  5FJ8 L;  5GAG c;  2CKC A;  1P7P A;  3S2D L;  2QL0 A;  2M6O A;  2JA7 L;  1IU6 A;  3S15 L;  3GTL L;  1DVB A;  2XJT A;  3VPB E;  2E2J L;  5M5W L;  2B63 L;  1SMM A;  4YWL A;  3I4M L;  1B2J A;  4POG A;  4C3J L;  3PO2 L;  1F4L A;  3HOW L;  6RXN A;  2A69 D;  3B0A B;  3MQK B;  2KKD A;  4BY7 L;  4XXB B;  4LHN A;  3LWO B;  3PKJ A;  1CAD A;  1VZH A;  3S2H L;  4BY1 L;  4AI3 A;  4X6A L;  3PL5 A;  1LTL A;  3PKI A;  4E6Y A;  2M6P A;  4RXN A;  4A3I L;  5C44 L;  1RYQ A;  4U67 1;  1ODH A;  1FHM A;  1Y1V L;  5IYB L;  2JI2 A;  5GAE c;  2NVQ L;  3HAX C;  5GAH c;  3HJW B;  4JAG A;  2A6E D;  1JYB A;  3HKZ P;  2K2D A;  5MFZ A;  3HOZ L;  2VUM L;  3HOY L;  5DM6 1;  3WWN B;  3PIP 1;  3K7A L;  1C09 A;  3GTQ L;  5IYD L;  2E2I L;  2WAQ P;  2JI1 A;  5EIO C;  5JVG 1;  4A3B L;  2ERJ A;  3PZA A;  2A68 D;  1Y1W L;  3A44 A;  3RYG A;  2O5J D;  5DM7 1;  2B5I D;  2M4V A;  4A3J L;  2Z3Q B;  5IY0 A;  4AHX A;  3B08 B;  3QQC E;  3KYW A;  3J7Y 1;  3S1R L;  5IP9 L;  1PFU A;  1YUX A;  5M5Y L;  5GAD c;  2ERS A;  5MLC 3;  3S1Q L;  3LWQ B;  3K35 A;  5C4J L;  4ZN1 B;  3FDJ A;  4A3E L;  4AI1 A;  1SMU A;  2WB1 P;  1K83 L;  2V0F A;  1IRO A;  1LKP A;  2Y0S P;  2XJV A;  4AR4 A;  1QCV A;  1TWC L;  3IU3 I;  3RZ6 A;  1R0I A;  5MGN A;  1OWC A;  2GMG A;  1PFW A;  1I6H L;  3P2A A;  3S1M L;  5RXN A;  3H3V M;  1I50 L;  1R0J A;  4A3C L;  2PSM C;  1I3Q L;  1VZG A;  3S17 L;  1DX8 A;  2R93 L;  2JA6 L;  1PFY A;  5FLM L;  3PO3 L;  3H97 A;  4C3I L;  2VL6 A;  3HOX L;  2R92 L;  3PWF A;  1PZX A;  1B13 A;  3S14 L;  4YWM A;  1YUZ A;  2XJP A;  4AHY A;  4A3F L;  2C6A A;  2MS3 A;  4Y7N L;  1NNQ A;  4Y52 L;  2JI3 A;  2A6H D;  2AUS B;  1R0F A;  1TWG L;  1CAA A;  5IYC L;  2BE5 D;  1TWH L;  4C2M 1;  4AR3 A;  3GTO L;  3WWL A;  2V3B B;  1R9T L;  1T9O A;  1R0G A;  4V19 6;  2V0E A;  4A3L L;  5IP7 L;  1QQT A;  4A3K L;  3RZD L;  1NXG A;  2YU9 L;  2DSX A;  3P8B A;  2AYJ A;  4UY8 1;  4AI2 A;  2RDV A;  1S24 A;  4AHW A;  1YV1 A;  1BQ8 A;  7RXN A;  5EIN C;  2L0Z A;  2E2H L;  2CR8 A;  3LWR B;  5AI2 A; 
#chains in the Genus database with same CATH homology
 2APO B;  3HJY B;  3LWV B;  2RFK B;  3HAX C;  3HJW B;  3LWO B;  3LWR B;  2HVY C;  2AQC A;  3MQK B;  2EY4 E;  3LWQ B;  3LWP B;  2AUS B; 
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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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