3FDS | Genus

Total Genus 58

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	58
sequence length	245
structure length	241
Chain Sequence	MMKAKVIDAVSFSYILRTVGDFLSEANFIVTKEGIRVSGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFKLEDVNDILKRVLKDDTLILSSNESKLTLTFDGEFTRSFELPLIQVESTQPLEFPFKAQLLTITFADIIDELSDLGEVLNIHSKENKLYFEVIGDLSTAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPRA

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/5cfedeb2c3a02958549d907c/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5cfedeb2c3a02958549d907c/pdb.gz): 1596 ms

reading 241 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

241 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:240});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	Transferase
source organism	Sulfolobus solfataricus
publication title	Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA pubmed doi rcsb
molecule keywords	DNA polymerase IV
total genus	58
structure length	241
sequence length	245
ec nomenclature
pdb deposition date	2008-11-26

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
D	PF00705	PCNA_N	Proliferating cell nuclear antigen, N-terminal domain
D	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	3fdsD00

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations