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


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