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


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