3LWPA

Structure of h/aca rnp bound to a substrate rna containing 5brdu
Total Genus 97
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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
97
sequence length
327
structure length
317
Chain Sequence
RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLW
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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 binding protein/rna
molecule keywords Pseudouridine synthase Cbf5
publication title Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study.
pubmed doi rcsb
source organism Pyrococcus furiosus
total genus 97
structure length 317
sequence length 327
ec nomenclature ec 5.4.99.25: tRNA pseudouridine(55) synthase.
pdb deposition date 2010-02-24

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 3lwpA01
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 3lwpA02
1KSLA 1KSVA 3HJYA 1R3FA 2HVYA 2APOA 1R3EA 1XPIA 3LWVA 1KSKA 3LWPA 3MQKA 1SGVA 1K8WA 3LWOA 4LGTA 1V9KA 3ZV0C 1ZE2A 3LWRA 3U28A 2AUSA 2AB4A 1PRZA 2RFKA 2ISTA 1V9FA 3UAIA 3DH3A 1ZE1A 3HAXA 2EY4A 4LABA 1ZL3A 2I82A 1QYUA 3HJWA 3LWQA
chains in the Genus database with same CATH superfamily
1KSLA 1WXWA 1XPIA 2DP9A 2FRXA 1SGVA 3LWPA 3MQKA 1SI7A 3C0KA 4DMGA 1V9KA 3ZV0C 3U28A 2Z0TA 1SZWA 1SQWA 2CX0A 1QYUA 2I82A 4CI1B 3HJWA 2CWWA 3IUWA 1Z2ZA 1KSVA 3HJYA 3M6VA 3M4XA 2B78A 1XNEA 3LJCA 4CI2B 3M65A 1PRZA 1T5YA 1IQ8A 1Q7HA 2J5VA 3DH3A 2ANEA 1ZS7A 3HAXA 1WK2A 1ZL3A 2J5TA 1ZBOA 3M6XA 2CX1A 1R3FA 2HVYA 1S04A 1SB7A 3LWVA 1KSKA 4TZ4C 4LGTA 1ZE2A 3LDFA 3LWRA 2RFKA 1V9FA 2P38A 4LABA 1UOYA 2E5OA 1IT7A 3M6UA 2KKUA 1IT8A 2APOA 4Q1TA 1R3EA 3M6WA 1K8WA 1TE7A 3D79A 1WXXA 2AUSA 2AB4A 2Q07A 2ISTA 3UAIA 3VSEA 1ZE1A 2EY4A 2AS0A 4CI3B 3LWOA 1J2BA 3LWQA
chains in the Genus database with same CATH topology
1KSLA 1KSVA 3HJYA 1R3FA 3M6VA 3M4XA 2HVYA 2APOA 1R3EA 1XPIA 1SB7A 2FRXA 3LWVA 1KSKA 3LWPA 3M6WA 3MQKA 1SGVA 1SI7A 1K8WA 4LGTA 1V9KA 3ZV0C 1ZE2A 3LWRA 3U28A 2AUSA 3M6UA 2AB4A 1PRZA 2RFKA 1SZWA 2ISTA 1V9FA 3UAIA 3DH3A 1ZE1A 2EY4A 3HAXA 4LABA 3HJWA 1UOYA 1ZL3A 2I82A 1QYUA 3LWOA 1Z2ZA 3M6XA 3LWQA
chains in the Genus database with same CATH homology


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