4TR6 | Genus

Total Genus 91

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	91
sequence length	380
structure length	380
Chain Sequence	SHMKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDDGVSFTGSDSDISIESFIPKEEGDKEIVTIEQPGSIVLQARFFSEIVKKLPMATVEIEVQNQYLTIIRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNLIRQTVFAVSTSETRPILTGVNWKVEQSELLCTATDSHRLALRKAKLDIPEDRSYNVVIPGKSLTELSKILDDNQELVDIVITETQVLFKAKNVLFFSRLLDGNYPDTTSLIPQDSKTEIIVNTKEFLQAIDRASLLAREGRNNVVKLSAKPAESIEISSNSPEIGKVVEAIVADQIEGEELNISFSPKYMLDALKVLEGAEIRVSFTGAMRPFLIRTPNDETIVQLILPVRTY

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/5d00b119a49f232387f849cb/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d00b119a49f232387f849cb/pdb.gz): 1428 ms

reading 380 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

380 atoms created

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

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:379});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

publication title	Differential Modes of Peptide Binding onto Replicative Sliding Clamps from Various Bacterial Origins. pubmed doi rcsb
molecule keywords	DNA polymerase III subunit beta
molecule tags	Dna binding protein
source organism	Bacillus subtilis
total genus	91
structure length	380
sequence length	380
chains with identical sequence	B
ec nomenclature	ec 2.7.7.7: DNA-directed DNA polymerase.
pdb deposition date	2014-06-14

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00712	DNA_pol3_beta	DNA polymerase III beta subunit, N-terminal domain
A	PF02767	DNA_pol3_beta_2	DNA polymerase III beta subunit, central domain
A	PF02768	DNA_pol3_beta_3	DNA polymerase III beta subunit, C-terminal domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.10.150.10	Alpha Beta	Roll	DNA Polymerase III; Chain A, domain 2	DNA Polymerase III, subunit A, domain 2	4tr6A01
3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen	Proliferating Cell Nuclear Antigen	4tr6A02

4N99A 3I2MX 4PNUA 4OVFA 5AH4A 4N9AA 5FVEA 3LX2A 5B7OA 3FDSC 1W60A 5JNED 2HIIA 3AIXB 5HACA 2HIIB 2ZVLA 3U61F 1GE8A 3V62B 1YYPA 3FDSD 3AIZA 1JQLA 2AVTA 3RB9A 3WGWA 3A1JC 3Q4JA 3U60F 3L0WA 3D1GA 2HIKA 5AGUA 4N98A 1B8HA 3U5ZF 4N95A 3G65A 5IWDA 2IO4A 5E0UA 3G65B 2IO4B 4D2GA 4MJQA 2IX2A 3PWEA 4MJPA 1MMIA 1U76A 2IX2B 1DMLA 4K3LA 2NTIC 1VPKA 3Q4KA 4N97A 4K3KA 3A2FB 5CFKA 2ZVKA 2IZOB 3GGRA 4CS5A 4K3SA 3F1VA 2NTIB 4YHRA 5A6DA 1T6LA 3HSLX 3TBLA 4K3PA 2HIIC 2POLA 4S3IA 1B77A 3P91A 4K3RA 1RXMA 3L0XA 3AIZC 4K74A 2ZVWA 2HIKB 4K3OA 4PNVA 1AXCA 1JQJA 4N94A 3P16A 3VKXA 3PGEB 1UL1A 3G65C 1VYMA 1PLRA 2IX2C 4ZTDA 3V60B 4L60A 5E0TA 3A1JA 3QSBA 2Z0LA 3A1JB 4TSZA 4L6PA 3GGRB 3LX1A 4HK1A 5IXAA 2IZOC 3L10A 3P87A 3D1EA 1RWZA 3HI8A 4N96A 2ZVVA 4RKIA 4PNWA 1RXZA 5DA7A 3P83A 3K4XA 2IJXA 1IZ4A 1CZDA 2XURA 3F1WA 1ISQA 3GPNA 5AUJA 5IY4A 2HIKC 2AWAA 2OD8A 4TR8A 3D1FA 5AGVA 5AH2A 1IZ5A 1VYJA 3V61B 4TR6A 3AIXA 4RJFA 1UD9A 5E0VA 5H0TA 4OVHA 5FRQA 3T0PA 4OVGA 2ZVMA 1PLQA 4MJRA 1U7BA 3QSBB 1OK7A 4K3QA 3GGRC 4TR7A 1SXJF 5DAIA 4K3MA 3IFVA 3GPMA 4TRTA 3BEPA 2NTIA 1UNNA 3Q4LA
chains in the Genus database with same CATH superfamily

4N99A 3I2MX 4PNUA 4OVFA 5AH4A 4N9AA 5FVEA 3LX2A 5B7OA 3FDSC 1W60A 5JNED 2HIIA 3AIXB 5HACA 2HIIB 2ZVLA 3U61F 1GE8A 3V62B 1YYPA 3FDSD 3AIZA 1JQLA 2AVTA 3RB9A 3WGWA 3A1JC 3Q4JA 3U60F 3L0WA 3D1GA 2HIKA 5AGUA 4N98A 1B8HA 3L0WB 3U5ZF 4N95A 3G65A 5IWDA 2IO4A 5E0UA 3G65B 2IO4B 4D2GA 4MJQA 2IX2A 3PWEA 4MJPA 1MMIA 1U76A 2IX2B 1DMLA 4K3LA 2NTIC 1VPKA 3Q4KA 4N97A 4K3KA 3A2FB 5CFKA 2ZVKA 2IZOB 3GGRA 4CS5A 4K3SA 3F1VA 2NTIB 4YHRA 5A6DA 1T6LA 3HSLX 3TBLA 4K3PA 2HIIC 2POLA 4S3IA 1B77A 3P91A 4K3RA 1RXMA 3L0XA 3AIZC 4K74A 3L0XB 2ZVWA 2HIKB 4K3OA 4PNVA 1AXCA 1JQJA 4N94A 3PGEA 3P16A 3VKXA 3PGEB 1UL1A 3G65C 1VYMA 1PLRA 2IX2C 4ZTDA 3V60B 4L60A 5E0TA 3A1JA 3QSBA 2Z0LA 3A1JB 4TSZA 4L6PA 3GGRB 3LX1A 4HK1A 5IXAA 2IZOC 3L10A 3P87A 3D1EA 1RWZA 3L10B 3HI8A 4N96A 2ZVVA 4RKIA 4PNWA 1RXZA 5DA7A 3P83A 3K4XA 2IJXA 1IZ4A 1CZDA 2XURA 3F1WA 1ISQA 3GPNA 5AUJA 5IY4A 2HIKC 2AWAA 2OD8A 4TR8A 3D1FA 5AGVA 5AH2A 1IZ5A 1VYJA 3V61B 4TR6A 3AIXA 4RJFA 1UD9A 5E0VA 5H0TA 4OVHA 5FRQA 3T0PA 4OVGA 2ZVMA 1PLQA 4MJRA 1U7BA 3QSBB 1OK7A 4K3QA 3GGRC 4TR7A 1SXJF 5DAIA 4K3MA 3IFVA 3GPMA 4TRTA 3BEPA 2NTIA 1UNNA 3Q4LA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4N99 A;  3I2M X;  4PNU A;  4OVF A;  5AH4 A;  4N9A A;  5FVE A;  3LX2 A;  5B7O A;  3FDS C;  1W60 A;  5JNE D;  2HII A;  3AIX B;  5HAC A;  2HII B;  2ZVL A;  3U61 F;  1GE8 A;  3V62 B;  1YYP A;  3FDS D;  3AIZ A;  1JQL A;  2AVT A;  3RB9 A;  3WGW A;  3A1J C;  3Q4J A;  3U60 F;  3L0W A;  3D1G A;  2HIK A;  5AGU A;  4N98 A;  1B8H A;  3U5Z F;  4N95 A;  3G65 A;  5IWD A;  2IO4 A;  5E0U A;  3G65 B;  2IO4 B;  4D2G A;  4MJQ A;  2IX2 A;  3PWE A;  4MJP A;  1MMI A;  1U76 A;  2IX2 B;  1DML A;  4K3L A;  2NTI C;  1VPK A;  3Q4K A;  4N97 A;  4K3K A;  3A2F B;  5CFK A;  2ZVK A;  2IZO B;  3GGR A;  4CS5 A;  4K3S A;  3F1V A;  2NTI B;  4YHR A;  5A6D A;  1T6L A;  3HSL X;  3TBL A;  4K3P A;  2HII C;  2POL A;  4S3I A;  1B77 A;  3P91 A;  4K3R A;  1RXM A;  3L0X A;  3AIZ C;  4K74 A;  2ZVW A;  2HIK B;  4K3O A;  4PNV A;  1AXC A;  1JQJ A;  4N94 A;  3P16 A;  3VKX A;  3PGE B;  1UL1 A;  3G65 C;  1VYM A;  1PLR A;  2IX2 C;  4ZTD A;  3V60 B;  4L60 A;  5E0T A;  3A1J A;  3QSB A;  2Z0L A;  3A1J B;  4TSZ A;  4L6P A;  3GGR B;  3LX1 A;  4HK1 A;  5IXA A;  2IZO C;  3L10 A;  3P87 A;  3D1E A;  1RWZ A;  3HI8 A;  4N96 A;  2ZVV A;  4RKI A;  4PNW A;  1RXZ A;  5DA7 A;  3P83 A;  3K4X A;  2IJX A;  1IZ4 A;  1CZD A;  2XUR A;  3F1W A;  1ISQ A;  3GPN A;  5AUJ A;  5IY4 A;  2HIK C;  2AWA A;  2OD8 A;  4TR8 A;  3D1F A;  5AGV A;  5AH2 A;  1IZ5 A;  1VYJ A;  3V61 B;  4TR6 A;  3AIX A;  4RJF A;  1UD9 A;  5E0V A;  5H0T A;  4OVH A;  5FRQ A;  3T0P A;  4OVG A;  2ZVM A;  1PLQ A;  4MJR A;  1U7B A;  3QSB B;  1OK7 A;  4K3Q A;  3GGR C;  4TR7 A;  1SXJ F;  5DAI A;  4K3M A;  3IFV A;  3GPM A;  4TRT A;  3BEP A;  2NTI A;  1UNN A;  3Q4L A; 
#chains in the Genus database with same CATH topology
 4N99 A;  3I2M X;  4PNU A;  4OVF A;  5AH4 A;  4N9A A;  5FVE A;  3LX2 A;  5B7O A;  3FDS C;  1W60 A;  5JNE D;  2HII A;  3AIX B;  5HAC A;  2HII B;  2ZVL A;  3U61 F;  1GE8 A;  3V62 B;  1YYP A;  3FDS D;  3AIZ A;  1JQL A;  2AVT A;  3RB9 A;  3WGW A;  3A1J C;  3Q4J A;  3U60 F;  3L0W A;  3D1G A;  2HIK A;  5AGU A;  4N98 A;  1B8H A;  3L0W B;  3U5Z F;  4N95 A;  3G65 A;  5IWD A;  2IO4 A;  5E0U A;  3G65 B;  2IO4 B;  4D2G A;  4MJQ A;  2IX2 A;  3PWE A;  4MJP A;  1MMI A;  1U76 A;  2IX2 B;  1DML A;  4K3L A;  2NTI C;  1VPK A;  3Q4K A;  4N97 A;  4K3K A;  3A2F B;  5CFK A;  2ZVK A;  2IZO B;  3GGR A;  4CS5 A;  4K3S A;  3F1V A;  2NTI B;  4YHR A;  5A6D A;  1T6L A;  3HSL X;  3TBL A;  4K3P A;  2HII C;  2POL A;  4S3I A;  1B77 A;  3P91 A;  4K3R A;  1RXM A;  3L0X A;  3AIZ C;  4K74 A;  3L0X B;  2ZVW A;  2HIK B;  4K3O A;  4PNV A;  1AXC A;  1JQJ A;  4N94 A;  3PGE A;  3P16 A;  3VKX A;  3PGE B;  1UL1 A;  3G65 C;  1VYM A;  1PLR A;  2IX2 C;  4ZTD A;  3V60 B;  4L60 A;  5E0T A;  3A1J A;  3QSB A;  2Z0L A;  3A1J B;  4TSZ A;  4L6P A;  3GGR B;  3LX1 A;  4HK1 A;  5IXA A;  2IZO C;  3L10 A;  3P87 A;  3D1E A;  1RWZ A;  3L10 B;  3HI8 A;  4N96 A;  2ZVV A;  4RKI A;  4PNW A;  1RXZ A;  5DA7 A;  3P83 A;  3K4X A;  2IJX A;  1IZ4 A;  1CZD A;  2XUR A;  3F1W A;  1ISQ A;  3GPN A;  5AUJ A;  5IY4 A;  2HIK C;  2AWA A;  2OD8 A;  4TR8 A;  3D1F A;  5AGV A;  5AH2 A;  1IZ5 A;  1VYJ A;  3V61 B;  4TR6 A;  3AIX A;  4RJF A;  1UD9 A;  5E0V A;  5H0T A;  4OVH A;  5FRQ A;  3T0P A;  4OVG A;  2ZVM A;  1PLQ A;  4MJR A;  1U7B A;  3QSB B;  1OK7 A;  4K3Q A;  3GGR C;  4TR7 A;  1SXJ F;  5DAI A;  4K3M A;  3IFV A;  3GPM A;  4TRT A;  3BEP A;  2NTI A;  1UNN A;  3Q4L A; 
#chains in the Genus database with same CATH homology
 4N99 A;  3I2M X;  4PNU A;  4OVF A;  5AH4 A;  4N9A A;  5FVE A;  3LX2 A;  5B7O A;  3FDS C;  1W60 A;  5JNE D;  2HII A;  3AIX B;  5HAC A;  2HII B;  2ZVL A;  3U61 F;  1GE8 A;  3V62 B;  1YYP A;  3FDS D;  3AIZ A;  1JQL A;  2AVT A;  3RB9 A;  3WGW A;  3A1J C;  3Q4J A;  3U60 F;  3L0W A;  3D1G A;  2HIK A;  5AGU A;  4N98 A;  1B8H A;  3U5Z F;  4N95 A;  3G65 A;  5IWD A;  2IO4 A;  5E0U A;  3G65 B;  2IO4 B;  4D2G A;  4MJQ A;  2IX2 A;  3PWE A;  4MJP A;  1MMI A;  1U76 A;  2IX2 B;  1DML A;  4K3L A;  2NTI C;  1VPK A;  3Q4K A;  4N97 A;  4K3K A;  3A2F B;  5CFK A;  2ZVK A;  2IZO B;  3GGR A;  4CS5 A;  4K3S A;  3F1V A;  2NTI B;  4YHR A;  5A6D A;  1T6L A;  3HSL X;  3TBL A;  4K3P A;  2HII C;  2POL A;  4S3I A;  1B77 A;  3P91 A;  4K3R A;  1RXM A;  3L0X A;  3AIZ C;  4K74 A;  2ZVW A;  2HIK B;  4K3O A;  4PNV A;  1AXC A;  1JQJ A;  4N94 A;  3P16 A;  3VKX A;  3PGE B;  1UL1 A;  3G65 C;  1VYM A;  1PLR A;  2IX2 C;  4ZTD A;  3V60 B;  4L60 A;  5E0T A;  3A1J A;  3QSB A;  2Z0L A;  3A1J B;  4TSZ A;  4L6P A;  3GGR B;  3LX1 A;  4HK1 A;  5IXA A;  2IZO C;  3L10 A;  3P87 A;  3D1E A;  1RWZ A;  3HI8 A;  4N96 A;  2ZVV A;  4RKI A;  4PNW A;  1RXZ A;  5DA7 A;  3P83 A;  3K4X A;  2IJX A;  1IZ4 A;  1CZD A;  2XUR A;  3F1W A;  1ISQ A;  3GPN A;  5AUJ A;  5IY4 A;  2HIK C;  2AWA A;  2OD8 A;  4TR8 A;  3D1F A;  5AGV A;  5AH2 A;  1IZ5 A;  1VYJ A;  3V61 B;  4TR6 A;  3AIX A;  4RJF A;  1UD9 A;  5E0V A;  5H0T A;  4OVH A;  5FRQ A;  3T0P A;  4OVG A;  2ZVM A;  1PLQ A;  4MJR A;  1U7B A;  3QSB B;  1OK7 A;  4K3Q A;  3GGR C;  4TR7 A;  1SXJ F;  5DAI A;  4K3M A;  3IFV A;  3GPM A;  4TRT A;  3BEP A;  2NTI A;  1UNN A;  3Q4L 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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4TR6A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations