3HJYA

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate rna
Total Genus 77
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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
77
sequence length
327
structure length
320
Chain Sequence
RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLW
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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 tags Isomerase/rna
molecule keywords pseudouridine synthase CBf5
publication title Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
pubmed doi rcsb
source organism Pyrococcus furiosus
total genus 77
structure length 320
sequence length 327
ec nomenclature ec 5.4.99.25: tRNA pseudouridine(55) synthase.
pdb deposition date 2009-05-22

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 3hjyA01
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 3hjyA02
3UAIA 1KSKA 3HJYA 1R3FA 1K8WA 2AB4A 3ZV0C 4LGTA 1V9FA 2I82A 3LWVA 1ZL3A 1XPIA 2ISTA 4LABA 3U28A 2HVYA 2EY4A 3LWOA 2RFKA 3LWRA 1KSVA 3LWPA 2APOA 1R3EA 1PRZA 1V9KA 1ZE1A 2AUSA 3MQKA 3LWQA 1QYUA 3DH3A 1KSLA 1SGVA 3HJWA 1ZE2A 3HAXA
chains in the Genus database with same CATH superfamily
3UAIA 1KSKA 3IUWA 1K8WA 1V9FA 3LWVA 1IT8A 2DP9A 1S04A 4LABA 3C0KA 3U28A 1SZWA 1UOYA 2RFKA 3M65A 1V9KA 3MQKA 1QYUA 1WK2A 3HJWA 1ZE2A 3HAXA 3M6XA 1R3FA 3M6UA 1SI7A 2AB4A 1XNEA 2E5OA 3LWPA 2APOA 4Q1TA 4TZ4C 1PRZA 1SB7A 2Z0TA 2AUSA 3LWQA 3DH3A 1ZBOA 1TE7A 1SGVA 3LJCA 3HJYA 3VSEA 4LGTA 3LDFA 1IQ8A 2Q07A 2KKUA 4CI1B 2ISTA 2CX0A 1WXWA 2ANEA 2P38A 2CX1A 2HVYA 4CI3B 3LWOA 3LWRA 1KSVA 2J5TA 1ZE1A 1J2BA 1Q7HA 1SQWA 2CWWA 2AS0A 3D79A 1Z2ZA 1WXXA 3ZV0C 2I82A 1ZL3A 1XPIA 1IT7A 2FRXA 1ZS7A 3M4XA 3M6WA 3M6VA 2EY4A 2J5VA 1R3EA 4DMGA 4CI2B 1KSLA 1T5YA 2B78A
chains in the Genus database with same CATH topology
3M6XA 3UAIA 1KSKA 3HJYA 1R3FA 3M6UA 1SI7A 2AB4A 1K8WA 1Z2ZA 3ZV0C 4LGTA 1V9FA 2I82A 3LWVA 1ZL3A 1XPIA 2FRXA 2ISTA 3M4XA 4LABA 3M6WA 3U28A 3M6VA 1SZWA 1UOYA 2HVYA 2EY4A 3LWOA 2RFKA 3LWRA 1KSVA 3LWPA 2APOA 1R3EA 1PRZA 1V9KA 1SB7A 1ZE1A 2AUSA 3MQKA 3LWQA 1QYUA 3DH3A 1KSLA 1SGVA 3HJWA 1ZE2A 3HAXA
chains in the Genus database with same CATH homology


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

 
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#similar chains, but unknotted
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