2HVYA

Crystal structure of an h/aca box rnp from pyrococcus furiosus
Total Genus 90

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

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
S16 (298-305)TI1 (13-16)TI2 (14-17)EMPTYS11 (243-245)S1 (21-23)TVIII1 (23-26)S14 (277-281)TI4 (31-34)TI3 (25-28)TI5 (37-40)AH5 (220-233)TI6 (38-41)AH1 (43-48)AH4 (183-194)S2 (49-56)S3 (78-80)AH8 (309-314)S4 (89-97)3H1 (98-99)TI8 (99-102)S7 (154-167)3H2 (102-105)TIV2 (140-143)TIV1 (105-108)TIV3 (143-153)TI9 (106-109)TII1 (178-181)S5 (111-119)AH3 (125-135)TII'1 (167-170)TIV4 (194-197)TI10 (214-217)TII'2 (208-211)S10 (211-212)TIV5 (281-284)AH6 (236-242)AH7 (263-268)S12 (255-258)3H4 (260-262)S13 (272-273)TII2 (285-288)S15 (288-294)TI12 (294-297)AH2 (62-73)TI7 (85-88)S6 (137-142)S8 (170-177)S9 (198-208)3H3 (246-250)3H5 (274-276)TI11 (250-253)Updating...
connected with : NaN
molecule tags Isomerase/biosynthetic protein/rna
source organism Pyrococcus furiosus
publication title Crystal structure of an H/ACA box ribonucleoprotein particle
pubmed doi rcsb
molecule keywords H/ACA 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
4LABA 2AUSA 1KSVA 3LWRA 3ZV0C 3LWQA 2RFKA 3LWVA 3U28A 3MQKA 1KSLA 3LWOA 2ISTA 1K8WA 3HJYA 2EY4A 1ZE2A 1SGVA 3DH3A 1KSKA 3HAXA 1R3FA 3HJWA 2AB4A 2HVYA 1ZE1A 1QYUA 1PRZA 1V9KA 1R3EA 2APOA 1XPIA 3UAIA 1V9FA 2I82A 1ZL3A 4LGTA 3LWPA
chains in the Genus database with same CATH superfamily
4DMGA 3ZV0C 2J5TA 3LWVA 3U28A 2ANEA 1KSLA 3LWOA 2B78A 1K8WA 2J5VA 1KSKA 3HAXA 1R3FA 4CI1B 2CX1A 1R3EA 2APOA 3C0KA 2I82A 2P38A 2DP9A 4CI2B 3M6WA 4LABA 3LDFA 3M6XA 2AUSA 1KSVA 2FRXA 3LWQA 2RFKA 2CX0A 2CWWA 2AS0A 1UOYA 2ISTA 3HJYA 3VSEA 4TZ4C 2E5OA 2AB4A 1IT7A 2HVYA 1QYUA 1V9KA 1V9FA 1XNEA 1ZL3A 3M65A 3LWPA 1SB7A 1Q7HA 1WXWA 3LWRA 3M6UA 4Q1TA 3D79A 1ZS7A 2EY4A 1ZE2A 3M4XA 1SGVA 3IUWA 1IT8A 1TE7A 1ZE1A 2KKUA 3M6VA 1PRZA 3UAIA 1SZWA 1S04A 3LJCA 1SQWA 3MQKA 1ZBOA 1WK2A 2Q07A 3DH3A 1SI7A 1IQ8A 2Z0TA 1WXXA 3HJWA 1J2BA 4CI3B 1XPIA 4LGTA 1T5YA 1Z2ZA
chains in the Genus database with same CATH topology
4LABA 3M6XA 2AUSA 1KSVA 2FRXA 3LWRA 1SB7A 3ZV0C 3LWQA 2RFKA 3LWVA 3U28A 3M6UA 3MQKA 1KSLA 1UOYA 3LWOA 2ISTA 1K8WA 3HJYA 2EY4A 1ZE2A 3M4XA 1SGVA 3DH3A 1SI7A 1KSKA 3HAXA 1R3FA 3HJWA 2AB4A 2HVYA 1ZE1A 1QYUA 1PRZA 3M6VA 1V9KA 1Z2ZA 1R3EA 2APOA 1XPIA 3UAIA 1V9FA 2I82A 1ZL3A 4LGTA 1SZWA 3LWPA 3M6WA
chains in the Genus database with same CATH homology


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

 
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