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


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