3LWPA

Structure of h/aca rnp bound to a substrate rna containing 5brdu
Total Genus 97
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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
97
sequence length
327
structure length
317
Chain Sequence
RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLW
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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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molecule keywords Pseudouridine synthase Cbf5
publication title Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study.
pubmed doi rcsb
source organism Pyrococcus furiosus
molecule tags Isomerase/rna binding protein/rna
total genus 97
structure length 317
sequence length 327
ec nomenclature ec 5.4.99.25: tRNA pseudouridine(55) synthase.
pdb deposition date 2010-02-24

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01472 PUA PUA domain
A PF01509 TruB_N TruB family pseudouridylate synthase (N terminal domain)
A PF08068 DKCLD DKCLD (NUC011) domain
A PF16198 TruB_C_2 tRNA pseudouridylate synthase B C-terminal domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.30.130.70 Mainly Beta Roll Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 3lwpA01
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 3lwpA02
3DH3A 1KSLA 2HVYA 1R3EA 2ISTA 1ZL3A 1R3FA 1KSKA 2RFKA 1XPIA 2I82A 1ZE2A 2APOA 1PRZA 1QYUA 2EY4A 3LWVA 3LWQA 3LWPA 3U28A 1SGVA 1ZE1A 2AB4A 3HJYA 3LWRA 3MQKA 3HJWA 3HAXA 3LWOA 3UAIA 1K8WA 3ZV0C 2AUSA 1KSVA 1V9FA 1V9KA 4LABA 4LGTA
chains in the Genus database with same CATH superfamily
1KSLA 1R3EA 1J2BA 1SQWA 1XNEA 1ZS7A 1T5YA 1QYUA 4CI3B 4DMGA 3C0KA 3M6WA 3U28A 2CX1A 3MQKA 3HJWA 2CX0A 3HAXA 1K8WA 1KSVA 2J5TA 1SI7A 1V9KA 4LABA 3DH3A 2HVYA 3IUWA 1S04A 3M6VA 2ISTA 1ZL3A 2AS0A 1R3FA 4TZ4C 2RFKA 1ZE2A 3M6XA 2KKUA 1PRZA 1Z2ZA 2ANEA 1IT7A 1IT8A 2E5OA 3LWQA 3LWPA 3LDFA 2AB4A 3HJYA 4CI1B 2FRXA 3LWOA 1V9FA 2P38A 1WXWA 4Q1TA 1WXXA 2B78A 4CI2B 2DP9A 1KSKA 1XPIA 2I82A 2Z0TA 3LWVA 1ZE1A 3LWRA 1SZWA 2AUSA 1SB7A 3M6UA 4LGTA 2J5VA 1UOYA 1Q7HA 2CWWA 3M4XA 1TE7A 2APOA 2Q07A 2EY4A 1ZBOA 1SGVA 3M65A 3VSEA 1IQ8A 3UAIA 1WK2A 3ZV0C 3D79A 3LJCA
chains in the Genus database with same CATH topology
3DH3A 1KSLA 2HVYA 1UOYA 1R3EA 3M6VA 2ISTA 1ZL3A 1R3FA 3M4XA 1KSKA 2RFKA 1XPIA 2I82A 1ZE2A 3M6XA 2APOA 1PRZA 1QYUA 1Z2ZA 2EY4A 3LWVA 3M6WA 3LWQA 3LWPA 3U28A 1SGVA 1ZE1A 2AB4A 3HJYA 3LWRA 3MQKA 3HJWA 3HAXA 2FRXA 3LWOA 3UAIA 1K8WA 3ZV0C 2AUSA 1KSVA 1SZWA 1SB7A 1SI7A 1V9KA 1V9FA 3M6UA 4LABA 4LGTA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3DH3 A;  1KSL A;  2HVY A;  1R3E A;  2IST A;  1ZL3 A;  1R3F A;  1KSK A;  2RFK A;  1XPI A;  2I82 A;  1ZE2 A;  2APO A;  1PRZ A;  1QYU A;  2EY4 A;  3LWV A;  3LWQ A;  3LWP A;  3U28 A;  1SGV A;  1ZE1 A;  2AB4 A;  3HJY A;  3LWR A;  3MQK A;  3HJW A;  3HAX A;  3LWO A;  3UAI A;  1K8W A;  3ZV0 C;  2AUS A;  1KSV A;  1V9F A;  1V9K A;  4LAB A;  4LGT A; 
#chains in the Genus database with same CATH topology
 1KSL A;  1R3E A;  1J2B A;  1SQW A;  1XNE A;  1ZS7 A;  1T5Y A;  1QYU A;  4CI3 B;  4DMG A;  3C0K A;  3M6W A;  3U28 A;  2CX1 A;  3MQK A;  3HJW A;  2CX0 A;  3HAX A;  1K8W A;  1KSV A;  2J5T A;  1SI7 A;  1V9K A;  4LAB A;  3DH3 A;  2HVY A;  3IUW A;  1S04 A;  3M6V A;  2IST A;  1ZL3 A;  2AS0 A;  1R3F A;  4TZ4 C;  2RFK A;  1ZE2 A;  3M6X A;  2KKU A;  1PRZ A;  1Z2Z A;  2ANE A;  1IT7 A;  1IT8 A;  2E5O A;  3LWQ A;  3LWP A;  3LDF A;  2AB4 A;  3HJY A;  4CI1 B;  2FRX A;  3LWO A;  1V9F A;  2P38 A;  1WXW A;  4Q1T A;  1WXX A;  2B78 A;  4CI2 B;  2DP9 A;  1KSK A;  1XPI A;  2I82 A;  2Z0T A;  3LWV A;  1ZE1 A;  3LWR A;  1SZW A;  2AUS A;  1SB7 A;  3M6U A;  4LGT A;  2J5V A;  1UOY A;  1Q7H A;  2CWW A;  3M4X A;  1TE7 A;  2APO A;  2Q07 A;  2EY4 A;  1ZBO A;  1SGV A;  3M65 A;  3VSE A;  1IQ8 A;  3UAI A;  1WK2 A;  3ZV0 C;  3D79 A;  3LJC A; 
#chains in the Genus database with same CATH homology
 3DH3 A;  1KSL A;  2HVY A;  1UOY A;  1R3E A;  3M6V A;  2IST A;  1ZL3 A;  1R3F A;  3M4X A;  1KSK A;  2RFK A;  1XPI A;  2I82 A;  1ZE2 A;  3M6X A;  2APO A;  1PRZ A;  1QYU A;  1Z2Z A;  2EY4 A;  3LWV A;  3M6W A;  3LWQ A;  3LWP A;  3U28 A;  1SGV A;  1ZE1 A;  2AB4 A;  3HJY A;  3LWR A;  3MQK A;  3HJW A;  3HAX A;  2FRX A;  3LWO A;  3UAI A;  1K8W A;  3ZV0 C;  2AUS A;  1KSV A;  1SZW A;  1SB7 A;  1SI7 A;  1V9K A;  1V9F A;  3M6U A;  4LAB A;  4LGT 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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