1K8WA

Crystal structure of the e. coli pseudouridine synthase trub bound to a t stem-loop rna
Total Genus 90
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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
90
sequence length
304
structure length
304
Chain Sequence
MDINGVLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATKFSQYLLDSDKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRGDIEQIPSMYSALKYQGKKLYEYARQGIEVPREARPITVYELLFIRHEGNELELEIHCSKGTYIRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLRELVEQAEQQDIPAAELLDPLLMPMDSPASDYPVVNLPLTSSVYFKNGNPVRTSGAPLEGLVRVTEGENGKFIGMGEIDDEGRVAPRRLVVEY
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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 Lyase/rna
molecule keywords 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP
publication title Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
pubmed doi rcsb
source organism Escherichia coli
total genus 90
structure length 304
sequence length 304
ec nomenclature ec 5.4.99.25: tRNA pseudouridine(55) synthase.
pdb deposition date 2001-10-25

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01509 TruB_N TruB family pseudouridylate synthase (N terminal domain)
A PF09157 TruB-C_2 Pseudouridine synthase II TruB, C-terminal
A PF16198 TruB_C_2 tRNA pseudouridylate synthase B C-terminal domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.30.130.10 Mainly Beta Roll Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 PUA domain 1k8wA02
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 1k8wA01
1V9KA 1ZS7A 1QYUA 2HVYA 2P38A 3HJYA 2RFKA 1K8WA 4LABA 3VSEA 1PRZA 1R3EA 1ZL3A 4DMGA 1ZE1A 3LWOA 3LWPA 3LWRA 3C0KA 1IT7A 2CWWA 3D79A 3HAXA 1R3FA 3LWVA 2CX1A 1KSKA 2AUSA 4Q1TA 1SQWA 3HJWA 1KSLA 2CX0A 3LWQA 2APOA 1WXWA 2EY4A 3LDFA 2J5TA 1ZE2A 1XPIA 3DH3A 1T5YA 2J5VA 1J2BA 1Q7HA 1IQ8A 3U28A 1V9FA 1WXXA 1KSVA 2ISTA 1IT8A 3MQKA 2AS0A 2AB4A 4LGTA 2B78A 1SGVA 2I82A 2Q07A 3UAIA
chains in the Genus database with same CATH superfamily
3HJYA 3IUWA 3VSEA 1R3EA 1ZE1A 3LWRA 2Z0TA 3HAXA 1R3FA 2DP9A 3M6UA 4CI1B 3M6WA 3LDFA 2J5TA 1ZE2A 1XPIA 4TZ4C 2J5VA 1IQ8A 3U28A 3M4XA 3MQKA 2AS0A 4LGTA 2ANEA 2I82A 3LJCA 1ZS7A 2P38A 1SZWA 2KKUA 1XNEA 1ZL3A 4DMGA 3LWOA 2CWWA 3LWVA 1SB7A 2AUSA 3ZV0C 3HJWA 2CX0A 3LWQA 2APOA 2EY4A 1T5YA 1Q7HA 1IT8A 1UOYA 1TE7A 3UAIA 1V9KA 4CI3B 2RFKA 1K8WA 1PRZA 4CI2B 3LWPA 3C0KA 1IT7A 3D79A 2CX1A 1KSKA 1ZBOA 4Q1TA 1KSLA 1WXWA 3DH3A 1S04A 1V9FA 1WXXA 1KSVA 2AB4A 1SGVA 2Q07A 2E5OA 1WK2A 2HVYA 3M65A 4LABA 1Z2ZA 1SQWA 3M6VA 1SI7A 1J2BA 2FRXA 2ISTA 2B78A 1QYUA 3M6XA
chains in the Genus database with same CATH topology
1V9KA 1ZS7A 1QYUA 2HVYA 2P38A 3HJYA 2RFKA 1K8WA 4LABA 1SZWA 1Z2ZA 3VSEA 1PRZA 1R3EA 1ZL3A 4DMGA 1ZE1A 3LWOA 3LWPA 3LWRA 3C0KA 1IT7A 2CWWA 3D79A 3HAXA 1R3FA 3LWVA 1SB7A 2CX1A 1KSKA 2AUSA 4Q1TA 1SQWA 3HJWA 1KSLA 2CX0A 3LWQA 1SI7A 2APOA 1WXWA 2EY4A 3LDFA 2J5TA 1ZE2A 1XPIA 3DH3A 1T5YA 2J5VA 1J2BA 1Q7HA 1IQ8A 3U28A 1V9FA 1WXXA 1KSVA 2ISTA 1IT8A 3MQKA 2AS0A 2AB4A 4LGTA 2B78A 1SGVA 2I82A 2Q07A 3UAIA
chains in the Genus database with same CATH homology


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