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
2WIWA 1IPIA 4QBOA 4FZ2A 1ZP7A 4QBLA 4TKKA 3DNXA 3IEYB 1R11A 3P1ZA 2VLDA 2OSTA 1F1ZA 1OB9A 3P1YA 3P1ZB 1T0FA 2INBA 3AJVA 3IF0X 1Y1OA 4QBNA 1Y88A 1RLVA 2ZYZA 2FCOA 2WCZA 3AJVB 2WJ0A 1A79A 3FOVA 1RZNA 2OKFA 2CV8A 5FDKA 1HH1A 2ZYZB 3IEYA 2GW6A 1OB8A 4TKDA 1R0VA 1XMXA 2WCWA 2WIZA 2EO0A 1GEFA 2GJWA
chains in the Genus database with same CATH superfamily
2WIWA 4QBLA 4ZQUA 1UWVA 2FKCA 2CZRA 1EWQA 2O8DB 3THWB 1WBDA 1RLVA 3AJVB 2OKFA 3K0SA 1HH1A 1OH5A 1NG9A 1R0VA 2O8FA 2WCWA 2O8BB 2EO0A 1GEFA 2GJWA 2IXSA 3IEYB 2O8EB 1E3MA 1OB9A 2FL3A 3P1ZB 2WTUA 1T0FA 2INBA 4E6ZA 3BT7A 2O8CB 2WCZA 2ZYZA 1A79A 2BH2A 2CV8A 5FDKA 3THYA 1OB8A 2FKHB 3THXB 2DBSA 1IPIA 4FZ2A 2W8MA 4TKKA 1WB9A 3DNXA 4DA2A 2O8DA 2OSTA 3THWA 4G6UA 1OH6A 2FWRA 2Z0RA 3P1YA 3AJVA 3IF0X 4QBNA 1OH8A 2WJ0A 1RZNA 2O8BA 4EV1A 3IEYA 4TKDA 2O8EA 1YNMA 1WBBA 2VS1A 4QBOA 3ZLJA 2O8FB 1ZP7A 4DAPA 1R11A 2FZ4A 3P1ZA 4DAVA 2VLDA 1F1ZA 2JJQA 1OH7A 2O8CA 1Y1OA 1Y88A 1NNEA 2FCOA 3THXA 1W7AA 3FOVA 4G6VA 2ZYZB 4LQEA 2GW6A 1XMXA 2FLCA 2WIZA 1FW6A 3THYB
chains in the Genus database with same CATH topology
2WIWA 1IPIA 4QBOA 4FZ2A 1ZP7A 4QBLA 4ZQUA 1UWVA 2W8MA 4TKKA 4DAPA 3DNXA 3IEYB 4DA2A 1R11A 3P1ZA 4DAVA 2VLDA 2OSTA 1F1ZA 4G6UA 1OB9A 2FKCA 2FL3A 2CZRA 2JJQA 2Z0RA 3P1YA 3P1ZB 1T0FA 2INBA 3AJVA 3IF0X 1Y1OA 4QBNA 2FLCA 1Y88A 4E6ZA 1RLVA 3BT7A 2ZYZA 2FCOA 2WCZA 3AJVB 2WJ0A 1A79A 3FOVA 1RZNA 2OKFA 2BH2A 4G6VA 2CV8A 5FDKA 4EV1A 1HH1A 2ZYZB 3IEYA 4LQEA 2GW6A 1OB8A 4TKDA 1YNMA 1R0VA 2FKHB 2IXSA 2DBSA 1XMXA 2VS1A 2WCWA 2WIZA 2EO0A 1GEFA 2GJWA
chains in the Genus database with same CATH homology


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