1GEFA

Crystal structure of the archaeal holliday junction resolvase hjc
Total Genus 32

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
32
sequence length
120
structure length
120
Chain Sequence
MYRKGAQAERELIKLLEKHGFAVVRSAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLAVKFLNVGWRFIEVSPKIEKFVFTPSSGVSLEVLLGIQKTLE

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.


  Genus data interpretation
Chord Diagram
AH1 (3-19)O1 (1-3)S1 (22-25)S5 (75-82)S6 (86-91)3H1 (27-29)TIV1 (29-32)S3 (42-50)TII1 (82-85)EMPTY3H2 (103-105)AH3 (109-113)3H3 (115-117)S2 (34-37)TIV2 (38-41)S4 (55-57)S7 (99-101)AH2 (59-72)Updating...
connected with : NaN
molecule tags Hydrolase
source organism Pyrococcus furiosus
publication title Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition.
pubmed doi rcsb
molecule keywords HOLLIDAY JUNCTION RESOLVASE
total genus 32
structure length 120
sequence length 120
chains with identical sequence B, D, E
ec nomenclature ec 3.1.22.4: Crossover junction endodeoxyribonuclease.
pdb deposition date 2000-11-08

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01870 Hjc Archaeal holliday junction resolvase (hjc)
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1350.10 Alpha Beta 3-Layer(aba) Sandwich Trna Endonuclease; Chain: A, domain 1 Trna Endonuclease; Chain: A, domain 1 1gefA00
5FDKA 3AJVA 3P1ZA 4QBOA 1R11A 2OSTA 1RLVA 2WCZA 3DNXA 3AJVB 1Y88A 3P1ZB 2ZYZA 2CV8A 1ZP7A 1F1ZA 2FCOA 1IPIA 2ZYZB 3P1YA 4QBNA 4TKDA 1A79A 2OKFA 2EO0A 4QBLA 1R0VA 1GEFA 4TKKA 2WIZA 2VLDA 2WJ0A 1RZNA 1T0FA 1HH1A 2GJWA 1XMXA 3IEYA 2GW6A 1Y1OA 2WCWA 1OB8A 2INBA 1OB9A 3FOVA 2WIWA
chains in the Genus database with same CATH superfamily
5FDKA 3AJVA 3P1ZA 4QBOA 1R11A 2OSTA 1RLVA 2WCZA 2CZRA 3DNXA 2W8MA 2IXSA 1Y88A 3AJVB 3P1ZB 4LQEA 2ZYZA 2CV8A 1ZP7A 2JJQA 1F1ZA 2FCOA 1IPIA 2ZYZB 3P1YA 4QBNA 4TKDA 1A79A 2FKCA 2FL3A 4ZQUA 2OKFA 2EO0A 4QBLA 1R0VA 1GEFA 3IF0X 4TKKA 4DA2A 2VLDA 2WIZA 1YNMA 1RZNA 2WJ0A 1T0FA 1HH1A 4G6UA 2GJWA 4EV1A 2Z0RA 1XMXA 3IEYA 1UWVA 3BT7A 3IEYB 2GW6A 2FKHB 1Y1OA 2WCWA 4DAVA 4E6ZA 2VS1A 1OB8A 2INBA 1OB9A 3FOVA 2FLCA 2BH2A 4G6VA 4DAPA 2WIWA 2DBSA
chains in the Genus database with same CATH topology
5FDKA 3AJVA 3P1ZA 4QBOA 1R11A 2OSTA 1RLVA 2WCZA 2CZRA 3DNXA 2W8MA 2IXSA 1Y88A 3AJVB 3P1ZB 4LQEA 2ZYZA 2CV8A 1ZP7A 2JJQA 1F1ZA 2FCOA 1IPIA 2ZYZB 3P1YA 4QBNA 4TKDA 1A79A 2FKCA 2FL3A 4ZQUA 2OKFA 2EO0A 4QBLA 1R0VA 1GEFA 3IF0X 4TKKA 4DA2A 2VLDA 2WIZA 1YNMA 1RZNA 2WJ0A 1T0FA 1HH1A 4G6UA 2GJWA 4EV1A 2Z0RA 1XMXA 3IEYA 1UWVA 3BT7A 3IEYB 2GW6A 2FKHB 1Y1OA 2WCWA 4DAVA 4E6ZA 2VS1A 1OB8A 2INBA 1OB9A 3FOVA 2FLCA 2BH2A 4G6VA 4DAPA 2WIWA 2DBSA
chains in the Genus database with same CATH homology

  
#chains in the Genus database with same CATH superfamily
 5FDK A;  3AJV A;  3P1Z A;  4QBO A;  1R11 A;  2OST A;  1RLV A;  2WCZ A;  3DNX A;  3AJV B;  1Y88 A;  3P1Z B;  2ZYZ A;  2CV8 A;  1ZP7 A;  1F1Z A;  2FCO A;  1IPI A;  2ZYZ B;  3P1Y A;  4QBN A;  4TKD A;  1A79 A;  2OKF A;  2EO0 A;  4QBL A;  1R0V A;  1GEF A;  4TKK A;  2WIZ A;  2VLD A;  2WJ0 A;  1RZN A;  1T0F A;  1HH1 A;  2GJW A;  1XMX A;  3IEY A;  2GW6 A;  1Y1O A;  2WCW A;  1OB8 A;  2INB A;  1OB9 A;  3FOV A;  2WIW A; 
#chains in the Genus database with same CATH topology
 5FDK A;  3AJV A;  3P1Z A;  4QBO A;  1R11 A;  2OST A;  1RLV A;  2WCZ A;  2CZR A;  3DNX A;  2W8M A;  2IXS A;  1Y88 A;  3AJV B;  3P1Z B;  4LQE A;  2ZYZ A;  2CV8 A;  1ZP7 A;  2JJQ A;  1F1Z A;  2FCO A;  1IPI A;  2ZYZ B;  3P1Y A;  4QBN A;  4TKD A;  1A79 A;  2FKC A;  2FL3 A;  4ZQU A;  2OKF A;  2EO0 A;  4QBL A;  1R0V A;  1GEF A;  3IF0 X;  4TKK A;  4DA2 A;  2VLD A;  2WIZ A;  1YNM A;  1RZN A;  2WJ0 A;  1T0F A;  1HH1 A;  4G6U A;  2GJW A;  4EV1 A;  2Z0R A;  1XMX A;  3IEY A;  1UWV A;  3BT7 A;  3IEY B;  2GW6 A;  2FKH B;  1Y1O A;  2WCW A;  4DAV A;  4E6Z A;  2VS1 A;  1OB8 A;  2INB A;  1OB9 A;  3FOV A;  2FLC A;  2BH2 A;  4G6V A;  4DAP A;  2WIW A;  2DBS A; 
#chains in the Genus database with same CATH homology
 5FDK A;  3AJV A;  3P1Z A;  4QBO A;  1R11 A;  2OST A;  1RLV A;  2WCZ A;  2CZR A;  3DNX A;  2W8M A;  2IXS A;  1Y88 A;  3AJV B;  3P1Z B;  4LQE A;  2ZYZ A;  2CV8 A;  1ZP7 A;  2JJQ A;  1F1Z A;  2FCO A;  1IPI A;  2ZYZ B;  3P1Y A;  4QBN A;  4TKD A;  1A79 A;  2FKC A;  2FL3 A;  4ZQU A;  2OKF A;  2EO0 A;  4QBL A;  1R0V A;  1GEF A;  3IF0 X;  4TKK A;  4DA2 A;  2VLD A;  2WIZ A;  1YNM A;  1RZN A;  2WJ0 A;  1T0F A;  1HH1 A;  4G6U A;  2GJW A;  4EV1 A;  2Z0R A;  1XMX A;  3IEY A;  1UWV A;  3BT7 A;  3IEY B;  2GW6 A;  2FKH B;  1Y1O A;  2WCW A;  4DAV A;  4E6Z A;  2VS1 A;  1OB8 A;  2INB A;  1OB9 A;  3FOV A;  2FLC A;  2BH2 A;  4G6V A;  4DAP A;  2WIW A;  2DBS A;
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

  
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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