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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publication title Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex.
pubmed doi rcsb
source organism Pyrococcus furiosus
molecule tags Isomerase/rna
molecule keywords guide RNA 1
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
3LWOA 3LWPA 1SGVA 3DH3A 2I82A 1KSVA 3LWVA 1ZL3A 1R3EA 1V9KA 1PRZA 2RFKA 1ZE1A 3LWQA 2AB4A 3MQKA 4LABA 3HAXA 1KSKA 4LGTA 1ZE2A 3HJWA 2AUSA 3LWRA 3HJYA 1KSLA 1QYUA 2ISTA 1R3FA 2APOA 2EY4A 3U28A 2HVYA 1XPIA 3ZV0C 1V9FA 1K8WA 3UAIA
chains in the Genus database with same CATH superfamily
3LWOA 1SGVA 3M6XA 1KSVA 1IT7A 2RFKA 4CI1B 3LWQA 1Z2ZA 1SB7A 4LABA 1KSKA 2KKUA 4Q1TA 3M4XA 3HJWA 2AUSA 1R3FA 2DP9A 2Q07A 2HVYA 1XPIA 3ZV0C 1K8WA 1SQWA 1J2BA 1SZWA 3LWPA 3IUWA 4CI2B 3LWVA 1ZL3A 1V9KA 2B78A 1SI7A 3MQKA 1IT8A 3HAXA 4LGTA 1T5YA 2FRXA 2J5VA 1ZE2A 3LWRA 1XNEA 1QYUA 2ISTA 2EY4A 3U28A 1V9FA 3UAIA 3LDFA 1IQ8A 1WXXA 2CX1A 4DMGA 3DH3A 3M6WA 1WXWA 1R3EA 3C0KA 2CWWA 2J5TA 3M6VA 2CX0A 3M6UA 1WK2A 2ANEA 1TE7A 2AS0A 3HJYA 2APOA 1Q7HA 2Z0TA 2I82A 1ZBOA 3LJCA 1S04A 3D79A 1PRZA 1ZE1A 1ZS7A 2E5OA 2AB4A 3VSEA 1KSLA 2P38A 3M65A 1UOYA 4CI3B 4TZ4C
chains in the Genus database with same CATH topology
3LWOA 1SZWA 3LWPA 1SGVA 3DH3A 2I82A 3M6WA 3M6XA 3LWVA 1KSVA 1ZL3A 1R3EA 1V9KA 1PRZA 2RFKA 1ZE1A 3LWQA 1Z2ZA 3M6VA 1SB7A 1SI7A 2AB4A 3MQKA 3M6UA 4LABA 3HAXA 1KSKA 4LGTA 2FRXA 1ZE2A 3M4XA 3HJWA 2AUSA 3LWRA 3HJYA 1KSLA 1QYUA 2ISTA 1R3FA 2APOA 2EY4A 1UOYA 3U28A 2HVYA 1XPIA 3ZV0C 1V9FA 1K8WA 3UAIA
chains in the Genus database with same CATH homology


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