5E8F | Genus

Total Genus 43

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	43
sequence length	147
structure length	147
Chain Sequence	KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

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/5d00ff1784c06aa91cdad652/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d00ff1784c06aa91cdad652/pdb.gz): 2242 ms

reading 147 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

147 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:146});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

Chord Diagram

molecule tags	Hydrolase
source organism	Homo sapiens
publication title	The N- and C-terminal ends of RPGR can bind to PDE6 delta. pubmed doi rcsb
molecule keywords	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodie
total genus	43
structure length	147
sequence length	147
chains with identical sequence	C
ec nomenclature
pdb deposition date	2015-10-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF05351	GMP_PDE_delta	GMP-PDE, delta subunit

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

cath code	Class	Architecture	Topology	Homology	Domain
2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII; Chain A, domain 1	GMP phosphodiesterase, delta subunit	5e8fA00

4JV8B 1KSGB 4GOKC 4JVBB 5TARB 3RBQA 3T5IA 4GOJC 4JV6B 1KSHB 4JHPB 5E80A 3GQQA 1KSJB 5E8FA 4JVFB 5F2UA 3T5GB 5TB5B 5L7KA
chains in the Genus database with same CATH superfamily

4JVBB 5IJUA 3T5IA 1GDFA 1KMTA 2JI0A 1FT0A 2VTCA 4MAIA 2JHTA 1RHOA 5ACJA 1FT3A 1AJWA 4OY7A 3EJAA 4EISB 2JHUA 4JVFB 5TB5B 4RE1A 4F38B 4ALCA 5AA7A 4D7UA 1KSGB 3L15A 2JHYA 2YOYA 5FTZA 2JHWA 2JHVA 5ACFA 5HNOA 2YOXA 1KSHB 5FOHA 3GQQA 5F2UA 3T5GB 3UAMA 4FMRA 5L7KA 4GBOA 2YOWA 4MAHA 3JUAA 2LHSA 2JHSA 4OY6A 3RBQA 4ALSA 4QI8A 5EMWA 1FSTA 5EMVA 4JV6B 4D7VA 1QVYA 2YETA 5FJQA 4EISA 4ALQA 4ALEA 5E8FA 2BXWA 5DQEA 2BEMA 4B5QA 2JHXA 3KYSA 1DS6B 4JV8B 4GOKC 5TARB 2JHZA 2BENA 5DQ8A 4EIRA 4GOJC 4A02A 1FSOA 5HGUA 3ZUDA 2XWXA 4ALTA 1HH4D 5HNPA 4JHPB 5E80A 4ALRA 1KSJB 5ACIA 1DOAB 5ACHA 3EIIA 4OY8A 2R5OA 5ACGA 4LN0A
chains in the Genus database with same CATH topology

4JV8B 1KSGB 4GOKC 4JVBB 5TARB 3RBQA 3T5IA 4GOJC 4JV6B 1KSHB 4JHPB 5E80A 3GQQA 1KSJB 5E8FA 4JVFB 5F2UA 3T5GB 5TB5B 5L7KA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 4JV8 B;  1KSG B;  4GOK C;  4JVB B;  5TAR B;  3RBQ A;  3T5I A;  4GOJ C;  4JV6 B;  1KSH B;  4JHP B;  5E80 A;  3GQQ A;  1KSJ B;  5E8F A;  4JVF B;  5F2U A;  3T5G B;  5TB5 B;  5L7K A; 
#chains in the Genus database with same CATH topology
 4JVB B;  5IJU A;  3T5I A;  1GDF A;  1KMT A;  2JI0 A;  1FT0 A;  2VTC A;  4MAI A;  2JHT A;  1RHO A;  5ACJ A;  1FT3 A;  1AJW A;  4OY7 A;  3EJA A;  4EIS B;  2JHU A;  4JVF B;  5TB5 B;  4RE1 A;  4F38 B;  4ALC A;  5AA7 A;  4D7U A;  1KSG B;  3L15 A;  2JHY A;  2YOY A;  5FTZ A;  2JHW A;  2JHV A;  5ACF A;  5HNO A;  2YOX A;  1KSH B;  5FOH A;  3GQQ A;  5F2U A;  3T5G B;  3UAM A;  4FMR A;  5L7K A;  4GBO A;  2YOW A;  4MAH A;  3JUA A;  2LHS A;  2JHS A;  4OY6 A;  3RBQ A;  4ALS A;  4QI8 A;  5EMW A;  1FST A;  5EMV A;  4JV6 B;  4D7V A;  1QVY A;  2YET A;  5FJQ A;  4EIS A;  4ALQ A;  4ALE A;  5E8F A;  2BXW A;  5DQE A;  2BEM A;  4B5Q A;  2JHX A;  3KYS A;  1DS6 B;  4JV8 B;  4GOK C;  5TAR B;  2JHZ A;  2BEN A;  5DQ8 A;  4EIR A;  4GOJ C;  4A02 A;  1FSO A;  5HGU A;  3ZUD A;  2XWX A;  4ALT A;  1HH4 D;  5HNP A;  4JHP B;  5E80 A;  4ALR A;  1KSJ B;  5ACI A;  1DOA B;  5ACH A;  3EII A;  4OY8 A;  2R5O A;  5ACG A;  4LN0 A; 
#chains in the Genus database with same CATH homology
 4JV8 B;  1KSG B;  4GOK C;  4JVB B;  5TAR B;  3RBQ A;  3T5I A;  4GOJ C;  4JV6 B;  1KSH B;  4JHP B;  5E80 A;  3GQQ A;  1KSJ B;  5E8F A;  4JVF B;  5F2U A;  3T5G B;  5TB5 B;  5L7K 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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5E8FA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations