2HVYA

Crystal structure of an h/aca box rnp from pyrococcus furiosus
Total Genus 90
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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
90
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 keywords H/ACA RNA
publication title Crystal structure of an H/ACA box ribonucleoprotein particle
pubmed doi rcsb
source organism Pyrococcus furiosus
molecule tags Isomerase/biosynthetic protein/rna
total genus 90
structure length 320
sequence length 327
ec nomenclature ec 5.4.99.25: tRNA pseudouridine(55) synthase.
pdb deposition date 2006-07-31

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 2hvyA01
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 2hvyA02
2AUSA 1KSVA 3MQKA 4LABA 1R3FA 3HAXA 1KSLA 1PRZA 3HJWA 1K8WA 2HVYA 3UAIA 3LWPA 2I82A 2ISTA 1ZL3A 1ZE1A 1ZE2A 1V9KA 2APOA 2RFKA 3DH3A 2AB4A 1R3EA 1KSKA 1XPIA 3LWOA 2EY4A 3LWVA 1QYUA 3ZV0C 3U28A 3LWRA 3LWQA 4LGTA 3HJYA 1SGVA 1V9FA
chains in the Genus database with same CATH superfamily
3HJWA 2ANEA 1WXWA 1Q7HA 1UOYA 3DH3A 2B78A 2CX1A 3LWQA 3D79A 4Q1TA 3HJYA 2AUSA 2J5TA 3HAXA 4DMGA 1XNEA 1Z2ZA 3M6VA 3UAIA 2KKUA 3VSEA 2I82A 2CWWA 1IT8A 1ZL3A 1V9KA 1IQ8A 3M65A 3LWOA 3LWVA 3M6WA 3LWRA 4CI1B 2DP9A 1V9FA 2J5VA 1KSVA 3IUWA 4TZ4C 1R3FA 1ZBOA 3M6XA 1WK2A 1ZS7A 2HVYA 2E5OA 1S04A 2P38A 3M6UA 2AS0A 2RFKA 2AB4A 1R3EA 1QYUA 4CI3B 1T5YA 1TE7A 4LGTA 3C0KA 2CX0A 4LABA 3MQKA 4CI2B 1KSLA 1PRZA 1SB7A 1K8WA 1SZWA 2Q07A 3LWPA 1SI7A 2ISTA 1IT7A 3LJCA 1ZE1A 1ZE2A 2APOA 3LDFA 1KSKA 1XPIA 2EY4A 2FRXA 2Z0TA 3ZV0C 1WXXA 3U28A 1J2BA 1SGVA 1SQWA 3M4XA
chains in the Genus database with same CATH topology
2AUSA 1KSVA 3MQKA 4LABA 1R3FA 3HAXA 1KSLA 1PRZA 1SB7A 3HJWA 1K8WA 3M6XA 1Z2ZA 1SZWA 3M6VA 2HVYA 3UAIA 3LWPA 1SI7A 2I82A 2ISTA 1ZL3A 1UOYA 1ZE1A 1ZE2A 3M6UA 2APOA 1V9KA 2RFKA 3DH3A 2AB4A 1R3EA 1KSKA 1XPIA 3LWOA 2EY4A 3LWVA 2FRXA 1QYUA 3ZV0C 3U28A 3M6WA 3LWRA 3LWQA 4LGTA 3HJYA 3M4XA 1SGVA 1V9FA
chains in the Genus database with same CATH homology


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