1R0VA

Structure determination of the dimeric endonuclease in a pseudo-face-centerd p21212 space group
Total Genus 79
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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
79
sequence length
244
structure length
244
Chain Sequence
DFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV
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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 Translation, hydrolase
molecule keywords tRNA-intron endonuclease
publication title Structure determination of a truncated dimeric splicing endonuclease in pseudo-face-centered space group P2(1)2(1)2.
pubmed doi rcsb
source organism Archaeoglobus fulgidus
total genus 79
structure length 244
sequence length 244
chains with identical sequence B, C, D
ec nomenclature ec 4.6.1.16: tRNA-intron lyase.
pdb deposition date 2003-09-23

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01974 tRNA_int_endo tRNA intron endonuclease, catalytic C-terminal domain
A PF02778 tRNA_int_endo_N tRNA intron endonuclease, N-terminal domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1170.20 Alpha Beta 3-Layer(aba) Sandwich MutS, DNA mismatch repair protein, domain I tRNA intron endonuclease, N-terminal domain 1r0vA02
3.40.1350.10 Alpha Beta 3-Layer(aba) Sandwich Trna Endonuclease; Chain: A, domain 1 Trna Endonuclease; Chain: A, domain 1 1r0vA03
3.40.1350.10 Alpha Beta 3-Layer(aba) Sandwich Trna Endonuclease; Chain: A, domain 1 Trna Endonuclease; Chain: A, domain 1 1r0vA01
3P1YA 3AJVB 2ZYZA 1OB9A 1ZP7A 3DNXA 2VLDA 1GEFA 1XMXA 1Y88A 4FZ2A 3P1ZA 4TKDA 4TKKA 5FDKA 1RZNA 2OSTA 2FCOA 2WIWA 2ZYZB 1Y1OA 2EO0A 3FOVA 1F1ZA 4QBOA 1T0FA 4QBLA 1A79A 2WCZA 2WJ0A 3IEYA 2GJWA 1R11A 3P1ZB 3AJVA 2OKFA 1IPIA 2CV8A 2INBA 1R0VA 2GW6A 1OB8A 2WIZA 2WCWA 1HH1A 1RLVA 4QBNA
chains in the Genus database with same CATH superfamily
4G6VA 1OB9A 1NNEA 1GEFA 1W7AA 1XMXA 3P1ZA 4EV1A 4TKKA 4E6ZA 4DA2A 4DAPA 4QBOA 4QBLA 1A79A 2O8FB 2OKFA 1OH6A 2CZRA 2CV8A 2INBA 1R0VA 1OB8A 1WBBA 1OH5A 2O8CB 4QBNA 1NG9A 4ZQUA 2ZYZA 2VLDA 2O8BB 2FZ4A 2WTUA 4FZ2A 3THYA 3THXA 4TKDA 5FDKA 3IEYB 2O8DA 2DBSA 2EO0A 3FOVA 3IF0X 1E3MA 3THXB 3P1ZB 3AJVA 2O8DB 1WBDA 2GW6A 1UWVA 2WCWA 3BT7A 1RLVA 1OH7A 3P1YA 3AJVB 2O8EA 2FKCA 4G6UA 1ZP7A 3DNXA 1EWQA 1Y88A 1RZNA 2ZYZB 2FWRA 1Y1OA 1OH8A 2WCZA 2Z0RA 3THWA 2WJ0A 3IEYA 2FLCA 1FW6A 2IXSA 1R11A 3THYB 2WIZA 3ZLJA 2FKHB 2FL3A 2O8FA 4LQEA 2OSTA 2FCOA 2VS1A 2O8EB 2W8MA 2WIWA 1F1ZA 1T0FA 3K0SA 2O8CA 2GJWA 4DAVA 2JJQA 2O8BA 1IPIA 2BH2A 1WB9A 1HH1A 3THWB 1YNMA
chains in the Genus database with same CATH topology
1YNMA 3P1YA 3AJVB 2FKCA 4ZQUA 4G6UA 2ZYZA 1OB9A 1ZP7A 3DNXA 4G6VA 2VLDA 2FL3A 1GEFA 1XMXA 1Y88A 4FZ2A 3P1ZA 4LQEA 4EV1A 4TKDA 4TKKA 5FDKA 1RZNA 3IEYB 2FKHB 2OSTA 4E6ZA 2FCOA 2VS1A 2W8MA 4DA2A 2DBSA 2WIWA 2ZYZB 1Y1OA 2EO0A 3FOVA 4DAPA 1F1ZA 4QBOA 1T0FA 4QBLA 1A79A 2WCZA 2Z0RA 2WJ0A 3IEYA 2GJWA 3IF0X 2FLCA 2IXSA 1R11A 3P1ZB 3AJVA 4DAVA 2OKFA 2CZRA 2JJQA 1IPIA 2CV8A 2BH2A 2INBA 1R0VA 2GW6A 1OB8A 2WIZA 1UWVA 2WCWA 1HH1A 3BT7A 1RLVA 4QBNA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3P1Y A;  3AJV B;  2ZYZ A;  1OB9 A;  1ZP7 A;  3DNX A;  2VLD A;  1GEF A;  1XMX A;  1Y88 A;  4FZ2 A;  3P1Z A;  4TKD A;  4TKK A;  5FDK A;  1RZN A;  2OST A;  2FCO A;  2WIW A;  2ZYZ B;  1Y1O A;  2EO0 A;  3FOV A;  1F1Z A;  4QBO A;  1T0F A;  4QBL A;  1A79 A;  2WCZ A;  2WJ0 A;  3IEY A;  2GJW A;  1R11 A;  3P1Z B;  3AJV A;  2OKF A;  1IPI A;  2CV8 A;  2INB A;  1R0V A;  2GW6 A;  1OB8 A;  2WIZ A;  2WCW A;  1HH1 A;  1RLV A;  4QBN A; 
#chains in the Genus database with same CATH topology
 4G6V A;  1OB9 A;  1NNE A;  1GEF A;  1W7A A;  1XMX A;  3P1Z A;  4EV1 A;  4TKK A;  4E6Z A;  4DA2 A;  4DAP A;  4QBO A;  4QBL A;  1A79 A;  2O8F B;  2OKF A;  1OH6 A;  2CZR A;  2CV8 A;  2INB A;  1R0V A;  1OB8 A;  1WBB A;  1OH5 A;  2O8C B;  4QBN A;  1NG9 A;  4ZQU A;  2ZYZ A;  2VLD A;  2O8B B;  2FZ4 A;  2WTU A;  4FZ2 A;  3THY A;  3THX A;  4TKD A;  5FDK A;  3IEY B;  2O8D A;  2DBS A;  2EO0 A;  3FOV A;  3IF0 X;  1E3M A;  3THX B;  3P1Z B;  3AJV A;  2O8D B;  1WBD A;  2GW6 A;  1UWV A;  2WCW A;  3BT7 A;  1RLV A;  1OH7 A;  3P1Y A;  3AJV B;  2O8E A;  2FKC A;  4G6U A;  1ZP7 A;  3DNX A;  1EWQ A;  1Y88 A;  1RZN A;  2ZYZ B;  2FWR A;  1Y1O A;  1OH8 A;  2WCZ A;  2Z0R A;  3THW A;  2WJ0 A;  3IEY A;  2FLC A;  1FW6 A;  2IXS A;  1R11 A;  3THY B;  2WIZ A;  3ZLJ A;  2FKH B;  2FL3 A;  2O8F A;  4LQE A;  2OST A;  2FCO A;  2VS1 A;  2O8E B;  2W8M A;  2WIW A;  1F1Z A;  1T0F A;  3K0S A;  2O8C A;  2GJW A;  4DAV A;  2JJQ A;  2O8B A;  1IPI A;  2BH2 A;  1WB9 A;  1HH1 A;  3THW B;  1YNM A; 
#chains in the Genus database with same CATH homology
 1YNM A;  3P1Y A;  3AJV B;  2FKC A;  4ZQU A;  4G6U A;  2ZYZ A;  1OB9 A;  1ZP7 A;  3DNX A;  4G6V A;  2VLD A;  2FL3 A;  1GEF A;  1XMX A;  1Y88 A;  4FZ2 A;  3P1Z A;  4LQE A;  4EV1 A;  4TKD A;  4TKK A;  5FDK A;  1RZN A;  3IEY B;  2FKH B;  2OST A;  4E6Z A;  2FCO A;  2VS1 A;  2W8M A;  4DA2 A;  2DBS A;  2WIW A;  2ZYZ B;  1Y1O A;  2EO0 A;  3FOV A;  4DAP A;  1F1Z A;  4QBO A;  1T0F A;  4QBL A;  1A79 A;  2WCZ A;  2Z0R A;  2WJ0 A;  3IEY A;  2GJW A;  3IF0 X;  2FLC A;  2IXS A;  1R11 A;  3P1Z B;  3AJV A;  4DAV A;  2OKF A;  2CZR A;  2JJQ A;  1IPI A;  2CV8 A;  2BH2 A;  2INB A;  1R0V A;  2GW6 A;  1OB8 A;  2WIZ A;  1UWV A;  2WCW A;  1HH1 A;  3BT7 A;  1RLV A;  4QBN A; 
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