4NGF | Genus

Total Genus 50

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	50
sequence length	298
structure length	260
Chain Sequence	QPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFMLSLQMLELITRLHQYIFSHILRYCVLPLNVVSTLDIDFKFMEDIEKSETKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHC

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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Viewer cachePut cache://localLOAD_/file/5d266eecfbd60e6f14eb9bb0/pdb.gz

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The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5d266eecfbd60e6f14eb9bb0/pdb.gz): 983 ms

reading 260 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

260 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:259});backbone only;select *;

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

molecule tags	Hydrolase/rna
source organism	Homo sapiens
publication title	A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer. pubmed doi rcsb
molecule keywords	Endoribonuclease Dicer
total genus	50
structure length	260
sequence length	298
chains with identical sequence	B, C, D
ec nomenclature	ec 3.1.26.3: Ribonuclease III.
pdb deposition date	2013-11-01

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02170	PAZ	PAZ domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.170.260.10	Mainly Beta	Beta Complex	paz domain	paz domain	4ngfA02

2L5DA 2L5CA 4W5RA 2FFLA 1T2SA 4NGBA 3O6EX 4Z4IA 1SI3A 4NH5A 4W5QA 1R4KA 1VYNA 4Z4HA 4NGGA 4OLAA 4Z4CA 4Z4GA 1R6ZA 4NGCA 4NH3A 2XFMA 4F3TA 3O7VX 4NH6A 5T7BA 4W5NA 3O3IX 3MJ0A 4W5OA 4NGDA 5JS2A 5KI6A 4OLBA 4Z4EA 4KRFA 3O7XA 2QVWA 4Z4FA 4NGFA 4NHAA 4KREA 1T2RA 5JS1A 3QIRA 4W5TA 1SI2A
chains in the Genus database with same CATH superfamily

2L5DA 2L5CA 4W5RA 2FFLA 1T2SA 3DLHA 3O6EX 4NGBA 4Z4IA 1SI3A 4W5QA 1R4KA 1VYNA 4NH5A 4Z4HA 4NGGA 4OLAA 4Z4CA 4Z4GA 3HJFA 4L1PA 1R6ZA 4NGCA 4NH3A 3F73A 2XFMA 3DLBA 4F3TA 1Z25A 3HK2A 3O7VX 4NH6A 3HO1A 5T7BA 4W5NA 3O3IX 3MJ0A 4L1UA 4W5OA 1Z26A 1U04A 4NGDA 5JS2A 5KI6A 3U1UA 2DB9A 4OLBA 4Z4EA 4KRFA 2BZEA 3O7XA 3HVRA 2QVWA 4Z4FA 4NGFA 3DA5A 1SI2A 4NHAA 4KREA 1T2RA 5JS1A 3QIRA 4W5TA 3HM9A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 2L5D A;  2L5C A;  4W5R A;  2FFL A;  1T2S A;  4NGB A;  3O6E X;  4Z4I A;  1SI3 A;  4NH5 A;  4W5Q A;  1R4K A;  1VYN A;  4Z4H A;  4NGG A;  4OLA A;  4Z4C A;  4Z4G A;  1R6Z A;  4NGC A;  4NH3 A;  2XFM A;  4F3T A;  3O7V X;  4NH6 A;  5T7B A;  4W5N A;  3O3I X;  3MJ0 A;  4W5O A;  4NGD A;  5JS2 A;  5KI6 A;  4OLB A;  4Z4E A;  4KRF A;  3O7X A;  2QVW A;  4Z4F A;  4NGF A;  4NHA A;  4KRE A;  1T2R A;  5JS1 A;  3QIR A;  4W5T A;  1SI2 A; 
#chains in the Genus database with same CATH topology
 2L5D A;  2L5C A;  4W5R A;  2FFL A;  1T2S A;  3DLH A;  3O6E X;  4NGB A;  4Z4I A;  1SI3 A;  4W5Q A;  1R4K A;  1VYN A;  4NH5 A;  4Z4H A;  4NGG A;  4OLA A;  4Z4C A;  4Z4G A;  3HJF A;  4L1P A;  1R6Z A;  4NGC A;  4NH3 A;  3F73 A;  2XFM A;  3DLB A;  4F3T A;  1Z25 A;  3HK2 A;  3O7V X;  4NH6 A;  3HO1 A;  5T7B A;  4W5N A;  3O3I X;  3MJ0 A;  4L1U A;  4W5O A;  1Z26 A;  1U04 A;  4NGD A;  5JS2 A;  5KI6 A;  3U1U A;  2DB9 A;  4OLB A;  4Z4E A;  4KRF A;  2BZE A;  3O7X A;  3HVR A;  2QVW A;  4Z4F A;  4NGF A;  3DA5 A;  1SI2 A;  4NHA A;  4KRE A;  1T2R A;  5JS1 A;  3QIR A;  4W5T A;  3HM9 A; 
#chains in the Genus database with same CATH homology
 2L5D A;  2L5C A;  4W5R A;  2FFL A;  1T2S A;  3DLH A;  3O6E X;  4NGB A;  4Z4I A;  1SI3 A;  4W5Q A;  1R4K A;  1VYN A;  4NH5 A;  4Z4H A;  4NGG A;  4OLA A;  4Z4C A;  4Z4G A;  3HJF A;  4L1P A;  1R6Z A;  4NGC A;  4NH3 A;  3F73 A;  2XFM A;  3DLB A;  4F3T A;  1Z25 A;  3HK2 A;  3O7V X;  4NH6 A;  3HO1 A;  5T7B A;  4W5N A;  3O3I X;  3MJ0 A;  4L1U A;  4W5O A;  1Z26 A;  1U04 A;  4NGD A;  5JS2 A;  5KI6 A;  3U1U A;  2DB9 A;  4OLB A;  4Z4E A;  4KRF A;  2BZE A;  3O7X A;  3HVR A;  2QVW A;  4Z4F A;  4NGF A;  3DA5 A;  1SI2 A;  4NHA A;  4KRE A;  1T2R A;  5JS1 A;  3QIR A;  4W5T A;  3HM9 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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4NGFA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations