2RFKA

Substrate rna positioning in the archaeal h/aca ribonucleoprotein complex
Total Genus 73
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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
73
sequence length
334
structure length
334
Chain Sequence
EVRRILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLAPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLWEKRD
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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 guide RNA 1
publication title Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex.
pubmed doi rcsb
source organism Pyrococcus furiosus
molecule tags Isomerase/rna
total genus 73
structure length 334
sequence length 334
ec nomenclature ec 5.4.99.25: tRNA pseudouridine(55) synthase.
pdb deposition date 2007-09-30

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 2rfkA01
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 2rfkA02
3HJYA 1ZE2A 1V9KA 3HJWA 1XPIA 3LWQA 1PRZA 1QYUA 3HAXA 2I82A 1K8WA 3DH3A 3LWRA 2EY4A 1KSLA 1KSVA 1SGVA 3UAIA 2APOA 3MQKA 1ZE1A 2HVYA 1ZL3A 2ISTA 1V9FA 3U28A 2AB4A 1R3EA 3LWOA 3ZV0C 1KSKA 3LWVA 4LGTA 1R3FA 2RFKA 2AUSA 4LABA 3LWPA
chains in the Genus database with same CATH superfamily
2ANEA 1Z2ZA 1ZE2A 1XPIA 3LWQA 2J5VA 1S04A 1K8WA 3M6WA 2E5OA 1SGVA 1ZBOA 4TZ4C 3MQKA 2CX0A 2B78A 1WK2A 3M65A 2ISTA 1IT8A 3LWOA 1WXXA 2RFKA 2AUSA 3LWPA 3C0KA 3LJCA 1ZS7A 1QYUA 3HAXA 3LWRA 1KSVA 1SB7A 1SQWA 2Q07A 1ZE1A 2HVYA 1V9FA 1TE7A 2J5TA 3ZV0C 1KSKA 3LWVA 4LGTA 1R3FA 4LABA 2AS0A 1V9KA 3HJWA 3M6UA 3M6XA 1PRZA 2I82A 3D79A 4CI1B 2EY4A 1KSLA 4CI2B 2FRXA 1ZL3A 1J2BA 2AB4A 1R3EA 1Q7HA 3IUWA 3M4XA 3HJYA 1SI7A 2CWWA 4CI3B 1IT7A 2KKUA 2P38A 4Q1TA 1XNEA 1WXWA 3M6VA 2CX1A 3DH3A 3VSEA 3UAIA 4DMGA 2APOA 2DP9A 1IQ8A 3LDFA 3U28A 2Z0TA 1SZWA 1UOYA 1T5YA
chains in the Genus database with same CATH topology
3M4XA 3HJYA 1Z2ZA 1SI7A 1V9KA 3HJWA 1ZE2A 1XPIA 3M6UA 3LWQA 3M6XA 1PRZA 1QYUA 3HAXA 2I82A 1K8WA 3M6VA 3DH3A 3LWRA 3M6WA 2EY4A 1KSLA 1KSVA 1SGVA 3UAIA 1SB7A 2APOA 3MQKA 1ZE1A 2FRXA 2HVYA 1ZL3A 2ISTA 1V9FA 3U28A 2AB4A 1R3EA 3LWOA 3ZV0C 1KSKA 3LWVA 1SZWA 1R3FA 2RFKA 2AUSA 4LABA 1UOYA 4LGTA 3LWPA
chains in the Genus database with same CATH homology


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