2VLD | Genus

Total Genus 47

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	47
sequence length	233
structure length	228
Chain Sequence	MRKVIIKENPSEEEIKELLDLAEKHGGVVTIFARCKVHYEGRAKSELGEGDRIIIIKPDGSFLIHQNKKREPVNWQPPGSKVTFKENSMISIRRRPYERLEVEIIEPYSLVVFLAEDYEESEAEMANLIFENPRVIEEGFKPIYREKPIRHGIVDVMGVDKDGNIVVLELKRRKADLHAVSQMKRYVDSLKEEYGENVRGILVAPSLTEGAKKLLEKEGLEFRKLEPP

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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

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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

molecule tags	Hydrolase
source organism	Pyrococcus abyssi
publication title	Structure and function of a novel endonuclease acting on branched DNA substrates. pubmed doi rcsb
molecule keywords	Endonuclease NucS
total genus	47
structure length	228
sequence length	233
chains with identical sequence	B
ec nomenclature	ec 3.1.-.-:
pdb deposition date	2008-01-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01939	NucS	Endonuclease NucS

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
2.70.180.20	Mainly Beta	Distorted Sandwich	Protein Yojf; Chain: A;	Protein Yojf; Chain: A;	2vldA01
3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease; Chain: A, domain 1	Trna Endonuclease; Chain: A, domain 1	2vldA02

4TKDA 1Y1OA 3AJVB 2OKFA 2CV8A 4QBLA 1XMXA 2WCWA 3P1ZB 1HH1A 1R11A 1ZP7A 2WJ0A 1OB8A 1IPIA 4QBNA 1RLVA 1Y88A 1T0FA 2VLDA 4TKKA 1A79A 3FOVA 2ZYZA 2GW6A 5FDKA 1OB9A 2GJWA 2EO0A 1RZNA 2INBA 3P1YA 2WIWA 2WCZA 2ZYZB 2WIZA 2OSTA 1F1ZA 3AJVA 1R0VA 3P1ZA 4QBOA 2FCOA 3DNXA 1GEFA 3IEYA
chains in the Genus database with same CATH superfamily

2W8MA 4TKDA 1Y1OA 4G6VA 3BT7A 3AJVB 2OKFA 2CV8A 1UWVA 4QBLA 1XMXA 2WCWA 3P1ZB 1HH1A 1R11A 1ZP7A 2VS1A 1OB8A 3IEYB 2WJ0A 2FKCA 2FL3A 1IPIA 4QBNA 1RLVA 1Y88A 2JJQA 4EV1A 1T0FA 2VLDA 4DA2A 4TKKA 2IXSA 1A79A 3FOVA 2ZYZA 4DAVA 2GW6A 4E6ZA 2DBSA 5FDKA 4G6UA 1OB9A 1NJHA 1YNMA 3IF0X 2EO0A 2GJWA 1RZNA 2Z0RA 4ZQUA 2INBA 2CZRA 3P1YA 4LQEA 2WIWA 2WCZA 2ZYZB 2WIZA 2OSTA 1F1ZA 3AJVA 1R0VA 2BH2A 3P1ZA 4QBOA 2FCOA 3DNXA 1GEFA 4DAPA 2FLCA 2FKHB 3IEYA
chains in the Genus database with same CATH topology

2W8MA 4TKDA 1Y1OA 4G6VA 3BT7A 3AJVB 2OKFA 2CV8A 1UWVA 4QBLA 1XMXA 2WCWA 3P1ZB 1HH1A 1R11A 1ZP7A 2VS1A 1OB8A 3IEYB 2WJ0A 2FKCA 2FL3A 1IPIA 4QBNA 1RLVA 1Y88A 2JJQA 4EV1A 1T0FA 2VLDA 4DA2A 4TKKA 2IXSA 1A79A 3FOVA 2ZYZA 4DAVA 2GW6A 4E6ZA 2DBSA 5FDKA 4G6UA 1OB9A 1YNMA 3IF0X 2GJWA 2EO0A 1RZNA 2Z0RA 4ZQUA 2INBA 2CZRA 3P1YA 4LQEA 2WIWA 2WCZA 2ZYZB 2WIZA 2OSTA 1F1ZA 3AJVA 1R0VA 2BH2A 3P1ZA 4QBOA 2FCOA 3DNXA 1GEFA 4DAPA 2FLCA 2FKHB 3IEYA
chains in the Genus database with same CATH homology

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations