3P1ZB

Crystal structure of the aperopyrum pernix rna splicing endonuclease
Total Genus 46
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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
46
sequence length
180
structure length
180
Chain Sequence
PIKASGVLIGDSVLVTDVEQARSLYSCGYYGQPLDVEKPRGADFEGPLRLSLIESLYLAEKGVLEVAKPDGSSVGVEDLRTAVRGNPRFSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVTRGGDVSYLMIDWFRP
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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 Hydrolase
molecule keywords Putative uncharacterized protein
publication title Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop
pubmed doi rcsb
source organism Aeropyrum pernix
total genus 46
structure length 180
sequence length 180
chains with identical sequence D, F, H, J, L
ec nomenclature ec 4.6.1.16: tRNA-intron lyase.
pdb deposition date 2010-10-01

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
B PF01974 tRNA_int_endo tRNA intron endonuclease, catalytic C-terminal domain
B 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 3p1zB01
3.40.1350.10 Alpha Beta 3-Layer(aba) Sandwich Trna Endonuclease; Chain: A, domain 1 Trna Endonuclease; Chain: A, domain 1 3p1zB02
4TKKA 3P1ZB 3IEYA 1IPIA 4TKDA 2WIWA 2ZYZB 1T0FA 2WCWA 4QBLA 5FDKA 2WJ0A 1HH1A 3AJVA 2VLDA 1GEFA 3P1YA 3DNXA 4QBNA 1Y88A 1R11A 2GW6A 2EO0A 2FCOA 3P1ZA 2INBA 1A79A 2ZYZA 2OKFA 4FZ2A 2WIZA 4QBOA 1ZP7A 1RZNA 1OB8A 3FOVA 1R0VA 1OB9A 2WCZA 2CV8A 2GJWA 3AJVB 1F1ZA 1Y1OA 1RLVA 2OSTA 1XMXA
chains in the Genus database with same CATH superfamily
4LQEA 2Z0RA 4TKKA 1UWVA 4G6VA 1FW6A 4TKDA 4EV1A 2WIWA 2WCWA 3THYA 2WJ0A 2IXSA 2VLDA 1OH8A 3THWB 1E3MA 1OH7A 2O8EB 2O8BA 4DAVA 2WIZA 4QBOA 2WCZA 3THXA 1F1ZA 2OSTA 2FZ4A 2O8CB 2BH2A 2FKCA 1EWQA 1OH5A 2ZYZB 1T0FA 2VS1A 4QBLA 5FDKA 1WB9A 2FWRA 2O8CA 4FZ2A 1OH6A 1OB8A 3THWA 1OB9A 2GJWA 2O8EA 3AJVB 1Y1OA 2JJQA 2O8FB 1IPIA 1HH1A 1GEFA 4QBNA 3K0SA 3IF0X 2GW6A 3ZLJA 4E6ZA 3BT7A 2ZYZA 2OKFA 1ZP7A 3FOVA 1R0VA 3IEYB 2CV8A 1XMXA 2W8MA 4G6UA 3P1ZB 3IEYA 2O8BB 4DA2A 2CZRA 3AJVA 1NG9A 2WTUA 3P1YA 3DNXA 1YNMA 1NNEA 2O8DB 1Y88A 1R11A 2O8FA 2EO0A 2FCOA 3P1ZA 2FLCA 3THXB 1WBDA 2INBA 2FKHB 1A79A 1RZNA 4DAPA 2O8DA 1W7AA 2FL3A 1WBBA 3THYB 2DBSA 4ZQUA 1RLVA
chains in the Genus database with same CATH topology
4LQEA 2Z0RA 2W8MA 4TKKA 1UWVA 4G6UA 2BH2A 3P1ZB 3IEYA 1IPIA 4G6VA 2FKCA 4TKDA 4EV1A 2WIWA 2ZYZB 1T0FA 2VS1A 2WCWA 4QBLA 4DA2A 2CZRA 2IXSA 1HH1A 5FDKA 3AJVA 2WJ0A 2VLDA 1GEFA 3P1YA 3DNXA 4QBNA 1YNMA 1Y88A 3IF0X 1R11A 2GW6A 2EO0A 4E6ZA 2FCOA 3P1ZA 2FLCA 2INBA 2FKHB 3BT7A 1A79A 2ZYZA 2OKFA 4DAVA 4FZ2A 2WIZA 4QBOA 1ZP7A 1RZNA 1OB8A 4DAPA 3FOVA 1R0VA 1OB9A 2WCZA 2FL3A 3IEYB 2CV8A 2GJWA 2DBSA 3AJVB 4ZQUA 1F1ZA 1Y1OA 1RLVA 2OSTA 2JJQA 1XMXA
chains in the Genus database with same CATH homology


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