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
source organism Escherichia coli
publication title Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
pubmed doi rcsb
molecule keywords 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP
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
1PRZA 3LWOA 1T5YA 2B78A 1IT8A 2CX0A 2J5VA 4LGTA 4Q1TA 3LWPA 3HJWA 1ZE2A 2I82A 3UAIA 2AB4A 2P38A 1SGVA 3LWVA 2APOA 2CWWA 1WXWA 3C0KA 1KSLA 1KSVA 2AUSA 3DH3A 1IT7A 3HJYA 1J2BA 3D79A 2Q07A 3MQKA 1ZL3A 1KSKA 3LWQA 1SQWA 1XPIA 3VSEA 2AS0A 1ZE1A 1R3FA 1V9FA 1R3EA 4LABA 2RFKA 3LDFA 1V9KA 4DMGA 3HAXA 1QYUA 2J5TA 1ZS7A 2HVYA 3LWRA 1IQ8A 1WXXA 2CX1A 2EY4A 3U28A 1Q7HA 2ISTA 1K8WA
chains in the Genus database with same CATH superfamily
3HJWA 1ZE2A 3UAIA 2E5OA 1SGVA 1WK2A 1WXWA 3C0KA 4CI3B 1KSLA 2AUSA 3DH3A 1ZBOA 1J2BA 1KSKA 3LWQA 4TZ4C 1R3FA 1SB7A 1SI7A 1QYUA 3LWRA 3M6VA 2ISTA 3LWOA 2B78A 2CX0A 1IT8A 2FRXA 3M65A 3LWPA 1TE7A 2ANEA 3LWVA 1KSVA 3MQKA 1ZL3A 1V9FA 3M4XA 1V9KA 2KKUA 2CX1A 2EY4A 3IUWA 1Q7HA 3M6XA 2J5VA 4Q1TA 2AB4A 2CWWA 1IT7A 4CI1B 3M6WA 3HJYA 3D79A 2Q07A 1Z2ZA 1SQWA 3VSEA 1ZE1A 1R3EA 4LABA 3LDFA 4DMGA 3HAXA 1UOYA 2J5TA 1IQ8A 2DP9A 3ZV0C 3LJCA 1PRZA 1T5YA 4LGTA 2I82A 2P38A 2APOA 1S04A 2Z0TA 3M6UA 1XPIA 2AS0A 2RFKA 1SZWA 1XNEA 2HVYA 1ZS7A 1WXXA 3U28A 4CI2B 1K8WA
chains in the Genus database with same CATH topology
1PRZA 3LWOA 1T5YA 2B78A 1IT8A 2CX0A 2J5VA 4LGTA 4Q1TA 3LWPA 3HJWA 1ZE2A 2I82A 3UAIA 2AB4A 2P38A 1SGVA 3LWVA 2APOA 2CWWA 1WXWA 3C0KA 1KSLA 1KSVA 2AUSA 3DH3A 1IT7A 3HJYA 1J2BA 3D79A 2Q07A 3MQKA 1ZL3A 1KSKA 3LWQA 1Z2ZA 1SQWA 1XPIA 3VSEA 2AS0A 1ZE1A 1R3FA 1V9FA 1R3EA 4LABA 2RFKA 3LDFA 1SZWA 1V9KA 4DMGA 1SB7A 3HAXA 1SI7A 1QYUA 2J5TA 1ZS7A 2HVYA 3LWRA 1IQ8A 1WXXA 2CX1A 2EY4A 3U28A 1Q7HA 2ISTA 1K8WA
chains in the Genus database with same CATH homology


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