3HAXA

Crystal structure of a substrate-bound gar1-minus h/aca rnp from pyrococcus furiosus
Total Genus 95
Loading diagram...

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
95
sequence length
329
structure length
329
Chain Sequence
RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLWEK
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
molecule tags Isomerase/biosynthetic protein/rna
molecule keywords Probable tRNA pseudouridine synthase B
publication title Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.
pubmed doi rcsb
source organism Pyrococcus furiosus
total genus 95
structure length 329
sequence length 329
ec nomenclature ec 5.4.99.25: tRNA pseudouridine(55) synthase.
pdb deposition date 2009-05-03

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 3haxA01
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 3haxA02
2APOA 3MQKA 1XPIA 1KSVA 3LWQA 3U28A 2ISTA 3LWPA 1QYUA 3UAIA 3HJYA 3HJWA 1ZE2A 3LWOA 2I82A 1K8WA 1ZL3A 4LABA 2RFKA 1ZE1A 2HVYA 1V9KA 1KSLA 4LGTA 3LWVA 2EY4A 1V9FA 1R3FA 2AB4A 1R3EA 3LWRA 1KSKA 3DH3A 2AUSA 3HAXA 1SGVA 3ZV0C 1PRZA
chains in the Genus database with same CATH superfamily
2E5OA 2J5TA 2FRXA 3MQKA 2DP9A 2P38A 1WXXA 3HJWA 1ZE2A 1IQ8A 3M4XA 2CWWA 1SB7A 3M65A 4LABA 1ZE1A 1KSLA 3M6UA 1V9FA 3LWRA 1IT8A 1XPIA 3IUWA 4CI1B 3U28A 2ISTA 3C0KA 4Q1TA 1QYUA 1Z2ZA 1S04A 2Z0TA 4LGTA 2J5VA 1ZBOA 3LJCA 2AUSA 2CX0A 1SGVA 1PRZA 1WK2A 1SQWA 1ZS7A 3VSEA 3LWPA 3HJYA 3D79A 3LWOA 4CI2B 2I82A 1ZL3A 2KKUA 2B78A 2HVYA 4CI3B 1V9KA 3LWVA 1J2BA 2EY4A 1Q7HA 1KSKA 3HAXA 2APOA 1KSVA 3LWQA 3M6VA 1WXWA 3M6WA 3UAIA 3M6XA 3LDFA 1UOYA 1K8WA 1SZWA 4DMGA 2RFKA 1SI7A 1IT7A 2ANEA 1TE7A 2AS0A 2Q07A 1R3FA 2CX1A 2AB4A 1R3EA 3DH3A 1T5YA 1XNEA 4TZ4C 3ZV0C
chains in the Genus database with same CATH topology
2APOA 2FRXA 3MQKA 1XPIA 1KSVA 3LWQA 3U28A 2ISTA 3M6VA 3LWPA 3M6WA 1QYUA 3UAIA 3HJYA 3M6XA 3HJWA 1ZE2A 3LWOA 3M4XA 2I82A 1UOYA 1K8WA 1SZWA 1ZL3A 1SB7A 1Z2ZA 4LABA 2RFKA 1ZE1A 1SI7A 2HVYA 1V9KA 1KSLA 4LGTA 3M6UA 3LWVA 2EY4A 1V9FA 1R3FA 2AB4A 1R3EA 3LWRA 1KSKA 3DH3A 2AUSA 3HAXA 1SGVA 3ZV0C 1PRZA
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...