1R11A

Structure determination of the dimeric endonuclease in a pseudo-face-centerd p21 space group
Total Genus 93
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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
93
sequence length
303
structure length
303
Chain Sequence
GGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV
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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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publication title Structure determination of a truncated dimeric splicing endonuclease in pseudo-face-centered space group P2(1)2(1)2.
pubmed doi rcsb
molecule tags Translation, hydrolase
source organism Archaeoglobus fulgidus
molecule keywords tRNA-intron endonuclease
total genus 93
structure length 303
sequence length 303
chains with identical sequence B
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 1r11A02
3.40.1350.10 Alpha Beta 3-Layer(aba) Sandwich Trna Endonuclease; Chain: A, domain 1 Trna Endonuclease; Chain: A, domain 1 1r11A03
3.40.1350.150 Alpha Beta 3-Layer(aba) Sandwich Trna Endonuclease; Chain: A, domain 1 Trna Endonuclease; Chain: A, domain 1 1r11A01
2INBA 1A79A 2WJ0A 2OSTA 1Y88A 2GW6A 4TKKA 1GEFA 1OB8A 4QBNA 4QBLA 1RLVA 2ZYZB 2WCZA 2ZYZA 1F1ZA 2OKFA 3P1YA 3DNXA 1HH1A 1OB9A 2VLDA 4FZ2A 1R0VA 1RZNA 3IF0X 3P1ZB 3FOVA 5FDKA 3P1ZA 1Y1OA 3AJVB 2EO0A 4TKDA 3AJVA 2GJWA 4QBOA 1IPIA 2WCWA 1T0FA 3IEYB 3IEYA 2WIWA 1XMXA 2CV8A 2WIZA 1R11A 2FCOA 1ZP7A
chains in the Genus database with same CATH superfamily
2WJ0A 1Y88A 2WTUA 2GW6A 1OH8A 4TKKA 1GEFA 1EWQA 1RLVA 1F1ZA 3P1YA 2FKHB 4FZ2A 4ZQUA 3P1ZA 2O8FB 2O8DB 4TKDA 2O8FA 3THXB 3THYB 2FLCA 1T0FA 4LQEA 4DAVA 2CV8A 2WIZA 4E6ZA 1A79A 2O8CB 2O8CA 1NNEA 2IXSA 1HH1A 1OB9A 1R0VA 1E3MA 1Y1OA 3AJVB 2O8EB 3AJVA 2O8EA 1IPIA 1FW6A 2O8DA 2WCWA 3THXA 1NG9A 1OH5A 3THYA 2FZ4A 2WIWA 2DBSA 1OB8A 4QBLA 2ZYZB 3THWB 2O8BB 2ZYZA 3THWA 2O8BA 3DNXA 4EV1A 1W7AA 2W8MA 3IF0X 2FL3A 4DA2A 1WB9A 4QBOA 2GJWA 2BH2A 4DAPA 2VS1A 2INBA 1OH6A 3ZLJA 2OSTA 1WBBA 3BT7A 4QBNA 1WBDA 2WCZA 2OKFA 1UWVA 2VLDA 1RZNA 2CZRA 3P1ZB 3FOVA 5FDKA 3K0SA 2EO0A 2Z0RA 4G6VA 2FWRA 4G6UA 2FKCA 3IEYB 3IEYA 1YNMA 2JJQA 1XMXA 1OH7A 1R11A 2FCOA 1ZP7A
chains in the Genus database with same CATH topology
2INBA 1A79A 2WJ0A 2OSTA 3BT7A 1Y88A 2GW6A 4TKKA 1GEFA 1OB8A 4QBNA 4QBLA 1RLVA 2ZYZB 2WCZA 2ZYZA 1F1ZA 2OKFA 3P1YA 3DNXA 1UWVA 2IXSA 1HH1A 1OB9A 2VLDA 2W8MA 4FZ2A 1R0VA 1RZNA 2CZRA 3P1ZB 3FOVA 3IF0X 2FKHB 2BH2A 4ZQUA 5FDKA 2FL3A 3P1ZA 1Y1OA 3AJVB 2EO0A 2Z0RA 4TKDA 4DA2A 3AJVA 2GJWA 4G6VA 4QBOA 1IPIA 4G6UA 2VS1A 2WCWA 4DAPA 2FLCA 1T0FA 3IEYB 4EV1A 2FKCA 4LQEA 3IEYA 1YNMA 4DAVA 2WIWA 2JJQA 1XMXA 2CV8A 2WIZA 2DBSA 1R11A 2FCOA 1ZP7A 4E6ZA
chains in the Genus database with same CATH homology


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