3TBL | Genus

Total Genus 59

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	59
sequence length	256
structure length	250
Chain Sequence	MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIE

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/5d030d56bd81710f1c822170/pdb.gz

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The Resolver thinks Pdb

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

Time for openFile(/file/5d030d56bd81710f1c822170/pdb.gz): 1313 ms

reading 250 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

250 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:249});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	Replication
source organism	Homo sapiens
publication title	Structure of monoubiquitinated PCNA: Implications for DNA polymerase switching and Okazaki fragment maturation. pubmed doi rcsb
molecule keywords	Proliferating cell nuclear antigen
total genus	59
structure length	250
sequence length	256
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2011-08-07

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00705	PCNA_N	Proliferating cell nuclear antigen, N-terminal domain
A	PF02747	PCNA_C	Proliferating cell nuclear antigen, C-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen	Proliferating Cell Nuclear Antigen	3tblA00

5AUJA 3K4XA 5E0VA 2ZVVA 1RXMA 2HIIC 1B77A 2IZOB 1AXCA 3FDSD 2AVTA 5JNED 4YHRA 3WGWA 3FDSC 3G65C 4HK1A 1W60A 3LX2A 1GE8A 1VYMA 2IJXA 5DA7A 3U61F 4L60A 1U7BA 3V61B 2HIKC 3A2FB 5DAIA 2ZVKA 3I2MX 2IX2A 3AIZC 2ZVMA 3AIXA 3P83A 3HSLX 1VYJA 2IX2B 1SXJF 3P91A 3P87A 1T6LA 3GGRC 3V62B 1PLQA 1U76A 1YYPA 4L6PA 5HACA 5IWDA 5CFKA 2NTIC 3F1WA 3VKXA 4D2GA 3GPMA 4CS5A 1RWZA 1UL1A 3TBLA 2OD8A 1CZDA 2HIKA 1UD9A 2Z0LA 3HI8A 3A1JC 3U60F 5B7OA 1ISQA 3AIZA 2HIKB 2HIIA 5IXAA 3AIXB 1PLRA 4ZTDA 5IY4A 1IZ5A 2HIIB 3IFVA 2IO4A 2IZOC 3GGRA 3G65A 5A6DA 3U5ZF 1DMLA 3GPNA 2IX2C 4RJFA 2IO4B 3GGRB 3G65B 5E0UA 3LX1A 2NTIA 2AWAA 1IZ4A 2ZVWA 1RXZA 5E0TA 2ZVLA 1B8HA 5H0TA 2NTIB 3V60B 3A1JA 4TR6A 3A1JB
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 5AUJ A;  3K4X A;  5E0V A;  2ZVV A;  1RXM A;  2HII C;  1B77 A;  2IZO B;  1AXC A;  3FDS D;  2AVT A;  5JNE D;  4YHR A;  3WGW A;  3FDS C;  3G65 C;  4HK1 A;  1W60 A;  3LX2 A;  1GE8 A;  1VYM A;  2IJX A;  5DA7 A;  3U61 F;  4L60 A;  1U7B A;  3V61 B;  2HIK C;  3A2F B;  5DAI A;  2ZVK A;  3I2M X;  2IX2 A;  3AIZ C;  2ZVM A;  3AIX A;  3P83 A;  3HSL X;  1VYJ A;  2IX2 B;  1SXJ F;  3P91 A;  3P87 A;  1T6L A;  3GGR C;  3V62 B;  1PLQ A;  1U76 A;  1YYP A;  4L6P A;  5HAC A;  5IWD A;  5CFK A;  2NTI C;  3F1W A;  3VKX A;  4D2G A;  3GPM A;  4CS5 A;  1RWZ A;  1UL1 A;  3TBL A;  2OD8 A;  1CZD A;  2HIK A;  1UD9 A;  2Z0L A;  3HI8 A;  3A1J C;  3U60 F;  5B7O A;  1ISQ A;  3AIZ A;  2HIK B;  2HII A;  5IXA A;  3AIX B;  1PLR A;  4ZTD A;  5IY4 A;  1IZ5 A;  2HII B;  3IFV A;  2IO4 A;  2IZO C;  3GGR A;  3G65 A;  5A6D A;  3U5Z F;  1DML A;  3GPN A;  2IX2 C;  4RJF A;  2IO4 B;  3GGR B;  3G65 B;  5E0U A;  3LX1 A;  2NTI A;  2AWA A;  1IZ4 A;  2ZVW A;  1RXZ A;  5E0T A;  2ZVL A;  1B8H A;  5H0T A;  2NTI B;  3V60 B;  3A1J A;  4TR6 A;  3A1J B; 
#chains in the Genus database with same CATH topology
 5AUJ A;  3K4X A;  5E0V A;  2ZVV A;  1RXM A;  2HII C;  1B77 A;  2IZO B;  1AXC A;  3FDS D;  2AVT A;  5JNE D;  4YHR A;  3WGW A;  3FDS C;  3G65 C;  4HK1 A;  1W60 A;  3LX2 A;  1GE8 A;  1VYM A;  2IJX A;  5DA7 A;  3U61 F;  4L60 A;  1U7B A;  3V61 B;  2HIK C;  3A2F B;  5DAI A;  2ZVK A;  3I2M X;  2IX2 A;  3AIZ C;  2ZVM A;  3AIX A;  3P83 A;  3HSL X;  1VYJ A;  2IX2 B;  1SXJ F;  3P91 A;  3P87 A;  1T6L A;  3GGR C;  3V62 B;  1PLQ A;  1U76 A;  1YYP A;  4L6P A;  5HAC A;  5IWD A;  5CFK A;  2NTI C;  3F1W A;  3VKX A;  4D2G A;  3GPM A;  4CS5 A;  1RWZ A;  1UL1 A;  3TBL A;  2OD8 A;  1CZD A;  2HIK A;  1UD9 A;  2Z0L A;  3HI8 A;  3A1J C;  3U60 F;  5B7O A;  1ISQ A;  3AIZ A;  2HIK B;  2HII A;  5IXA A;  3AIX B;  1PLR A;  4ZTD A;  5IY4 A;  1IZ5 A;  2HII B;  3IFV A;  2IO4 A;  2IZO C;  3GGR A;  3G65 A;  5A6D A;  3U5Z F;  1DML A;  3GPN A;  2IX2 C;  4RJF A;  2IO4 B;  3GGR B;  3G65 B;  5E0U A;  3LX1 A;  2NTI A;  2AWA A;  1IZ4 A;  2ZVW A;  1RXZ A;  5E0T A;  2ZVL A;  1B8H A;  5H0T A;  2NTI B;  3V60 B;  3A1J A;  4TR6 A;  3A1J B; 
#chains in the Genus database with same CATH homology
 5AUJ A;  3K4X A;  5E0V A;  2ZVV A;  1RXM A;  2HII C;  1B77 A;  2IZO B;  1AXC A;  3FDS D;  2AVT A;  5JNE D;  4YHR A;  3WGW A;  3FDS C;  3G65 C;  4HK1 A;  1W60 A;  3LX2 A;  1GE8 A;  1VYM A;  2IJX A;  5DA7 A;  3U61 F;  4L60 A;  1U7B A;  3V61 B;  2HIK C;  3A2F B;  5DAI A;  2ZVK A;  3I2M X;  2IX2 A;  3AIZ C;  2ZVM A;  3AIX A;  3P83 A;  3HSL X;  1VYJ A;  2IX2 B;  1SXJ F;  3P91 A;  3P87 A;  1T6L A;  3GGR C;  3V62 B;  1PLQ A;  1U76 A;  1YYP A;  4L6P A;  5HAC A;  5IWD A;  5CFK A;  2NTI C;  3F1W A;  3VKX A;  4D2G A;  3GPM A;  4CS5 A;  1RWZ A;  1UL1 A;  3TBL A;  2OD8 A;  1CZD A;  2HIK A;  1UD9 A;  2Z0L A;  3HI8 A;  3A1J C;  3U60 F;  5B7O A;  1ISQ A;  3AIZ A;  2HIK B;  2HII A;  5IXA A;  3AIX B;  1PLR A;  4ZTD A;  5IY4 A;  1IZ5 A;  2HII B;  3IFV A;  2IO4 A;  2IZO C;  3GGR A;  3G65 A;  5A6D A;  3U5Z F;  1DML A;  3GPN A;  2IX2 C;  4RJF A;  2IO4 B;  3GGR B;  3G65 B;  5E0U A;  3LX1 A;  2NTI A;  2AWA A;  1IZ4 A;  2ZVW A;  1RXZ A;  5E0T A;  2ZVL A;  1B8H A;  5H0T A;  2NTI B;  3V60 B;  3A1J A;  4TR6 A;  3A1J B;

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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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3TBLA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations