1R3EA

Crystal structure of trna pseudouridine synthase trub and its rna complex: rna-protein recognition through a combination of rigid docking and induced fit
Total Genus 76
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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
76
sequence length
309
structure length
305
Chain Sequence
b'MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKERVLTLRKVFNTR'
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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(*CP*UP*GP*UP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)
publication title Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA Recognition Through a Combination of Rigid Docking and Induced Fit
pubmed doi rcsb
source organism Thermotoga maritima
molecule tags Lyase/rna
total genus 76
structure length 305
sequence length 309
ec nomenclature ec 5.4.99.25: tRNA pseudouridine(55) synthase.
pdb deposition date 2003-10-01

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01472 PUA PUA domain
A PF01509 TruB_N TruB family pseudouridylate synthase (N terminal domain)
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 1r3eA02
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 1r3eA01
1V9KA 4Q1TA 2EY4A 2I82A 1ZE2A 2AB4A 3UAIA 1SGVA 2B78A 1SQWA 3LDFA 3LWRA 4LABA 2CWWA 1KSLA 2J5TA 2RFKA 3DH3A 1KSKA 1PRZA 1J2BA 1IT7A 1WXWA 1IQ8A 2CX0A 1WXXA 1QYUA 4DMGA 1K8WA 4LGTA 3HJYA 1R3EA 1R3FA 3LWQA 2AS0A 1XPIA 2ISTA 1ZL3A 3LWOA 3LWPA 3U28A 3MQKA 1ZS7A 3VSEA 2J5VA 3HAXA 1IT8A 1ZE1A 1T5YA 3HJWA 2CX1A 3C0KA 2AUSA 3LWVA 1KSVA 3D79A 1Q7HA 2P38A 2HVYA 2APOA 2Q07A 1V9FA
chains in the Genus database with same CATH superfamily
2I82A 3LWRA 3M6WA 2E5OA 2J5TA 1IT7A 1IQ8A 1WXXA 1K8WA 3HJYA 1R3EA 1R3FA 2AS0A 2ISTA 1UOYA 3LWOA 1SZWA 3MQKA 3IUWA 1Q7HA 2P38A 2APOA 2FRXA 4Q1TA 1ZE2A 1SQWA 1Z2ZA 4CI2B 1TE7A 1J2BA 1QYUA 4TZ4C 3M6UA 1XNEA 3U28A 1ZE1A 2AUSA 1WK2A 1S04A 2HVYA 1SB7A 1V9KA 2EY4A 2AB4A 4CI3B 3UAIA 3LDFA 2CWWA 1KSLA 3DH3A 2CX0A 4DMGA 4LGTA 3LJCA 3LWPA 1XPIA 1ZL3A 3VSEA 2J5VA 1IT8A 3M4XA 3HJWA 3C0KA 2ANEA 3LWVA 1V9FA 2DP9A 1SI7A 1SGVA 2B78A 2Z0TA 3M6VA 4LABA 2RFKA 4CI1B 1KSKA 1PRZA 1WXWA 3ZV0C 3M65A 3LWQA 3M6XA 1ZBOA 1ZS7A 3HAXA 1T5YA 2CX1A 2KKUA 1KSVA 3D79A 2Q07A
chains in the Genus database with same CATH topology
1V9KA 4Q1TA 2EY4A 2I82A 1ZE2A 2AB4A 1SI7A 3UAIA 1SGVA 2B78A 1SQWA 3LDFA 1Z2ZA 3LWRA 4LABA 2CWWA 1KSLA 2J5TA 2RFKA 3DH3A 1KSKA 1PRZA 1J2BA 1IT7A 1WXWA 1IQ8A 2CX0A 1WXXA 1QYUA 4DMGA 1K8WA 4LGTA 3HJYA 1R3EA 1R3FA 3LWQA 2AS0A 1XPIA 2ISTA 1ZL3A 3LWOA 1SZWA 3LWPA 3U28A 3MQKA 1ZS7A 3VSEA 2J5VA 3HAXA 1IT8A 1ZE1A 1T5YA 3HJWA 2CX1A 3C0KA 2AUSA 3LWVA 1KSVA 3D79A 1Q7HA 2P38A 1SB7A 2HVYA 2APOA 2Q07A 1V9FA
chains in the Genus database with same CATH homology


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