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


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