4YHR | Genus

Total Genus 53

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	53
sequence length	256
structure length	256
Chain Sequence	MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFND

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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The Resolver thinks Pdb

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Time for openFile(/file/5d00ed40ebe5e7f7ded50d0c/pdb.gz): 1066 ms

reading 256 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

256 atoms created

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

Time for creating model: 24 ms

Adding embedded #jmolscript: select ({0:255});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	Dna binding protein
source organism	Saccharomyces cerevisiae (strain atcc 204508 / s288c)
publication title	Dead-End Elimination with a Polarizable Force Field Repacks PCNA Models from Low-Resolution X-ray Diffraction into Atomic Resolution Structures rcsb
molecule keywords	Proliferating cell nuclear antigen
total genus	53
structure length	256
sequence length	256
ec nomenclature
pdb deposition date	2015-02-27

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	4yhrA00

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations