1VPKA

Crystal structure of dna polymerase iii, beta subunit (tm0262) from thermotoga maritima at 2.00 a resolution
Total Genus 101
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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
101
sequence length
367
structure length
367
Chain Sequence
HMKVTVTTLELKDKITIASKALAKKSVKPILAGFLFEVKDGNFYICATDLETGVKATVNAAEISGEARFVVPGDVIQKMVKVLPDEITELSLEGDALVISSGSTVFRITTMPADEFPEITPAESGITFEVDTSLLEEMVEKVIFAAAKDEFMRNLNGVFWELHKNLLRLVASDGFRLALAEEQIENEEEASFLLSLKSMKEVQNVLDNTTEPTITVRYDGRRVSLSTNDVETVMRVVDAEFPDYKRVIPETFKTKVVVSRKELRESLKRVMVIASKGSESVKFEIEENVMRLVSKSPDYGEVVDEVEVQKEGEDLVIAFNPKFIEDVLKHIETEEIEMNFVDSTSPCQINPLDISGYLYIVMPIRLA
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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

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Transferase
molecule keywords DNA polymerase III, beta subunit
publication title Crystal structure of DNA polymerase III, beta subunit (TM0262) from Thermotoga maritima at 2.00 A resolution
rcsb
source organism Thermotoga maritima
total genus 101
structure length 367
sequence length 367
ec nomenclature ec 2.7.7.7: DNA-directed DNA polymerase.
pdb deposition date 2004-11-09

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
ClassArchitectureTopologyHomologyDomain
3.10.150.10 Alpha Beta Roll DNA Polymerase III; Chain A, domain 2 DNA Polymerase III, subunit A, domain 2 1vpkA01
3.10.150.10 Alpha Beta Roll DNA Polymerase III; Chain A, domain 2 DNA Polymerase III, subunit A, domain 2 1vpkA02
3.10.150.10 Alpha Beta Roll DNA Polymerase III; Chain A, domain 2 DNA Polymerase III, subunit A, domain 2 1vpkA03
4PNUA 4PNWA 1JQJA 3QSBA 2AVTA 1MMIA 3PGEB 4N94A 4N97A 3RB9A 4K3PA 5AH2A 5AGVA 1JQLA 1UNNA 4K3KA 4K3MA 4K3OA 4N95A 4TR7A 4PNVA 1VPKA 4TR6A 3Q4JA 3Q4LA 3PWEA 3Q4KA 3L0XA 3P16A 3QSBB 4K3LA 3F1VA 4K3RA 4K3SA 4MJQA 4N99A 4K74A 4MJRA 4N98A 5AH4A 3T0PA 3L0WA 3BEPA 4TR8A 4MJPA 5AGUA 4TRTA 4TSZA 5FRQA 4S3IA 4OVFA 5FVEA 1OK7A 4K3QA 2POLA 2AWAA 3D1FA 3D1GA 4OVGA 4OVHA 4N96A 2XURA 3L10A 4RKIA 3D1EA 4N9AA
chains in the Genus database with same CATH superfamily
4PNUA 3L0WB 4PNWA 1JQJA 3QSBA 2AVTA 1MMIA 3PGEB 4N94A 4N97A 3RB9A 4K3PA 3L10B 5AH2A 5AGVA 1JQLA 1UNNA 4K3KA 4K3MA 4K3OA 4N95A 4TR7A 4PNVA 1VPKA 4TR6A 3Q4JA 3Q4LA 3PWEA 3Q4KA 3L0XA 3P16A 3QSBB 4K3LA 3F1VA 4K3RA 4K3SA 4MJQA 4N99A 4K74A 4MJRA 4N98A 5AH4A 3T0PA 3L0WA 3BEPA 4TR8A 4MJPA 5AGUA 4TRTA 4TSZA 5FRQA 3PGEA 4S3IA 4OVFA 5FVEA 1OK7A 4K3QA 2POLA 2AWAA 3D1FA 3D1GA 4OVGA 4OVHA 4N96A 2XURA 3L10A 4RKIA 3D1EA 3L0XB 4N9AA
chains in the Genus database with same CATH topology
4PNUA 4PNWA 1JQJA 3QSBA 2AVTA 1MMIA 3PGEB 4N94A 4N97A 3RB9A 4K3PA 5AH2A 5AGVA 1JQLA 1UNNA 4K3KA 4K3MA 4K3OA 4N95A 4TR7A 4PNVA 1VPKA 4TR6A 3Q4JA 3Q4LA 3PWEA 3Q4KA 3L0XA 3P16A 3QSBB 4K3LA 3F1VA 4K3RA 4K3SA 4MJQA 4N99A 4K74A 4MJRA 4N98A 5AH4A 3T0PA 3L0WA 3BEPA 4TR8A 4MJPA 5AGUA 4TRTA 4TSZA 5FRQA 4S3IA 4OVFA 5FVEA 1OK7A 4K3QA 2POLA 2AWAA 3D1FA 3D1GA 4OVGA 4OVHA 4N96A 2XURA 3L10A 4RKIA 3D1EA 4N9AA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4PNU A;  4PNW A;  1JQJ A;  3QSB A;  2AVT A;  1MMI A;  3PGE B;  4N94 A;  4N97 A;  3RB9 A;  4K3P A;  5AH2 A;  5AGV A;  1JQL A;  1UNN A;  4K3K A;  4K3M A;  4K3O A;  4N95 A;  4TR7 A;  4PNV A;  1VPK A;  4TR6 A;  3Q4J A;  3Q4L A;  3PWE A;  3Q4K A;  3L0X A;  3P16 A;  3QSB B;  4K3L A;  3F1V A;  4K3R A;  4K3S A;  4MJQ A;  4N99 A;  4K74 A;  4MJR A;  4N98 A;  5AH4 A;  3T0P A;  3L0W A;  3BEP A;  4TR8 A;  4MJP A;  5AGU A;  4TRT A;  4TSZ A;  5FRQ A;  4S3I A;  4OVF A;  5FVE A;  1OK7 A;  4K3Q A;  2POL A;  2AWA A;  3D1F A;  3D1G A;  4OVG A;  4OVH A;  4N96 A;  2XUR A;  3L10 A;  4RKI A;  3D1E A;  4N9A A; 
#chains in the Genus database with same CATH topology
 4PNU A;  3L0W B;  4PNW A;  1JQJ A;  3QSB A;  2AVT A;  1MMI A;  3PGE B;  4N94 A;  4N97 A;  3RB9 A;  4K3P A;  3L10 B;  5AH2 A;  5AGV A;  1JQL A;  1UNN A;  4K3K A;  4K3M A;  4K3O A;  4N95 A;  4TR7 A;  4PNV A;  1VPK A;  4TR6 A;  3Q4J A;  3Q4L A;  3PWE A;  3Q4K A;  3L0X A;  3P16 A;  3QSB B;  4K3L A;  3F1V A;  4K3R A;  4K3S A;  4MJQ A;  4N99 A;  4K74 A;  4MJR A;  4N98 A;  5AH4 A;  3T0P A;  3L0W A;  3BEP A;  4TR8 A;  4MJP A;  5AGU A;  4TRT A;  4TSZ A;  5FRQ A;  3PGE A;  4S3I A;  4OVF A;  5FVE A;  1OK7 A;  4K3Q A;  2POL A;  2AWA A;  3D1F A;  3D1G A;  4OVG A;  4OVH A;  4N96 A;  2XUR A;  3L10 A;  4RKI A;  3D1E A;  3L0X B;  4N9A A; 
#chains in the Genus database with same CATH homology
 4PNU A;  4PNW A;  1JQJ A;  3QSB A;  2AVT A;  1MMI A;  3PGE B;  4N94 A;  4N97 A;  3RB9 A;  4K3P A;  5AH2 A;  5AGV A;  1JQL A;  1UNN A;  4K3K A;  4K3M A;  4K3O A;  4N95 A;  4TR7 A;  4PNV A;  1VPK A;  4TR6 A;  3Q4J A;  3Q4L A;  3PWE A;  3Q4K A;  3L0X A;  3P16 A;  3QSB B;  4K3L A;  3F1V A;  4K3R A;  4K3S A;  4MJQ A;  4N99 A;  4K74 A;  4MJR A;  4N98 A;  5AH4 A;  3T0P A;  3L0W A;  3BEP A;  4TR8 A;  4MJP A;  5AGU A;  4TRT A;  4TSZ A;  5FRQ A;  4S3I A;  4OVF A;  5FVE A;  1OK7 A;  4K3Q A;  2POL A;  2AWA A;  3D1F A;  3D1G A;  4OVG A;  4OVH A;  4N96 A;  2XUR A;  3L10 A;  4RKI A;  3D1E A;  4N9A 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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