3P1YA

Crystal structure of the chimeric archaeoglobus fulgidus rna splicing endonuclease with the broadest substrate specificity
Total Genus 99
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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
99
sequence length
314
structure length
314
Chain Sequence
IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGILSDEYVITKQTEIFSRYFYGSPLDVEKPRGADFEGPVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV
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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 tRNA-splicing endonuclease
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 Archaeoglobus fulgidus
total genus 99
structure length 314
sequence length 314
chains with identical sequence B, C, D
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
A PF01974 tRNA_int_endo tRNA intron endonuclease, catalytic C-terminal domain
A PF02778 tRNA_int_endo_N tRNA intron endonuclease, N-terminal domain
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 3p1yA02
3.40.1350.10 Alpha Beta 3-Layer(aba) Sandwich Trna Endonuclease; Chain: A, domain 1 Trna Endonuclease; Chain: A, domain 1 3p1yA03
3.40.1350.150 Alpha Beta 3-Layer(aba) Sandwich Trna Endonuclease; Chain: A, domain 1 Trna Endonuclease; Chain: A, domain 1 3p1yA01
1T0FA 1Y1OA 4TKDA 2OSTA 1R11A 1A79A 3IF0X 4QBLA 3FOVA 4FZ2A 1GEFA 2OKFA 3P1YA 2GJWA 1RLVA 1F1ZA 2VLDA 2WIZA 3P1ZA 3P1ZB 1OB8A 3AJVA 1RZNA 3AJVB 1OB9A 2ZYZA 2WJ0A 2FCOA 2ZYZB 2WCWA 1IPIA 2EO0A 3DNXA 2WCZA 2CV8A 5FDKA 1XMXA 4TKKA 3IEYA 3IEYB 1R0VA 4QBNA 1ZP7A 1HH1A 2INBA 4QBOA 2GW6A 2WIWA 1Y88A
chains in the Genus database with same CATH superfamily
1T0FA 2OSTA 2FLCA 3FOVA 2O8DA 2OKFA 2O8CB 3P1ZA 1OH7A 1OB8A 1RZNA 3AJVB 2O8EA 2ZYZA 2WCWA 3DNXA 2WCZA 4G6UA 2CV8A 5FDKA 2O8BB 4DAVA 2VS1A 3IEYB 4EV1A 1R0VA 1ZP7A 2INBA 4QBOA 4E6ZA 2WIWA 3THWA 1Y1OA 4G6VA 3THXB 4TKDA 1R11A 1A79A 2BH2A 4DA2A 1UWVA 2O8CA 3K0SA 1RLVA 2WIZA 1OH5A 1NNEA 3AJVA 2O8FB 2FWRA 2CZRA 2FCOA 1IPIA 2EO0A 2O8BA 1XMXA 3IEYA 3BT7A 3THYA 2FKCA 3THXA 4DAPA 3IF0X 2W8MA 4QBLA 2FZ4A 1WBBA 2O8FA 2FL3A 1OB9A 2WJ0A 2IXSA 4LQEA 4QBNA 1HH1A 4ZQUA 4FZ2A 1GEFA 2O8DB 3P1YA 2GJWA 1F1ZA 2VLDA 1YNMA 3P1ZB 1EWQA 3ZLJA 2O8EB 1NG9A 2DBSA 2ZYZB 2WTUA 1WBDA 1WB9A 2FKHB 1FW6A 1E3MA 4TKKA 3THYB 1W7AA 2GW6A 1OH6A 1OH8A 3THWB 2Z0RA 1Y88A 2JJQA
chains in the Genus database with same CATH topology
1T0FA 1Y1OA 4G6VA 4ZQUA 4TKDA 4DAPA 1R11A 2FLCA 1A79A 3IF0X 2W8MA 4QBLA 2OSTA 2BH2A 3FOVA 4DA2A 4FZ2A 1UWVA 1GEFA 2OKFA 3P1YA 2GJWA 1RLVA 1F1ZA 2VLDA 2WIZA 3P1ZA 1YNMA 3P1ZB 1OB8A 3AJVA 1RZNA 3AJVB 2FL3A 2CZRA 1OB9A 2DBSA 2ZYZA 2FCOA 2ZYZB 2IXSA 1IPIA 2EO0A 2WCWA 2WJ0A 3DNXA 2WCZA 4G6UA 2CV8A 5FDKA 4DAVA 2FKHB 1XMXA 2VS1A 4TKKA 3IEYA 4LQEA 3IEYB 4EV1A 1R0VA 3BT7A 4QBNA 1ZP7A 1HH1A 2INBA 4QBOA 2GW6A 4E6ZA 2WIWA 2FKCA 2Z0RA 1Y88A 2JJQA
chains in the Genus database with same CATH homology


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