4RKIA

Crystal structure of sliding beta clamp from helicobacter pylori
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
374
structure length
374
Chain Sequence
MKISVSKNDLENALRYLQAFLDKKDASSIASHIHLEVIKEKLFLKASDSDIGLKSYIFTQSSDKEGVGTINGKKFLDIISCLKDSNIILETKDDSLAIKQNKSSFKLPMFDADEFPEFPVIDPKVSIEVNAPFLVDAFKKIAPVIEQTSHKRELAGILMQFDQKHQTLSVVGTDTKRLSYTQLEKISIHSTEEDISCILPKRALLEILKLFYENFSFKSDGMLAVIENEMHTFFTKLIDGNYPDYQKILPKEYISSFTLGKEEFKESIKLCSSLSSTIKLTLEKNNALFESLDSEHSETAKTSVEIEKGLDIEKAFHLGVNAKFFLEALNALGTTQFVLRCNEPSSPFLIQESLDEKQSHLNAKISTLMMPITL
5010015020025030035035030025020015010050
020406080Genus Matrix

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
EMPTYS6 (87-92)AH2 (73-82)S1 (3-7)AH1 (8-18)TI1 (23-26)S5 (67-72)3H1 (19-21)AH4 (202-211)3H2 (30-32)TVIII1 (24-27)TI2 (26-29)S2 (33-39)TI'1 (39-42)S4 (52-65)TI9 (229-232)S16 (224-229)TIV1 (93-96)S8 (104-109)S7 (96-101)TII'1 (101-104)S13 (189-191)S9 (126-130)S15 (216-220)AH3 (133-142)S14 (195-201)3H4 (143-145)TI4 (147-150)TVIII4 (150-153)TI5 (152-155)S10 (157-163)TVIII5 (191-194)3H5 (164-166)TIV2 (184-187)S11 (168-175)S25 (367-370)TI8 (175-178)AH6 (323-332)S12 (178-184)TI13 (355-358)TVIII7 (254-257)S18 (257-261)TVIII9 (335-338)AH5 (262-273)TI10 (273-276)TIV5 (292-295)S22 (316-322)S19 (278-284)TI11 (284-287)TVIII8 (307-310)S21 (302-306)S20 (287-292)TII1 (296-299)S24 (349-353)TI12 (344-347)TII2 (353-356)TIV7 (360-363)S3 (42-49)S17 (232-237)TI3 (49-52)TVIII3 (124-127)TIV3 (220-223)S23 (337-341)3H3 (113-115)3H6 (246-248)Updating...
connected with : NaN
molecule tags Transferase
source organism Helicobacter pylori 26695
publication title Structural insight into beta-Clamp and its interaction with DNA Ligase in Helicobacter pylori.
pubmed doi rcsb
molecule keywords DNA polymerase III subunit beta
total genus 91
structure length 374
sequence length 374
ec nomenclature ec 2.7.7.7: DNA-directed DNA polymerase.
pdb deposition date 2014-10-13

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 4rkiA02
1JQLA 3L10A 3P16A 3RB9A 3PGEB 3QSBA 2XURA 3Q4KA 3Q4LA 4K3OA 4N94A 3D1FA 1MMIA 4N99A 4N96A 4TR6A 4RKIA 4MJPA 3BEPA 4TR7A 5AGVA 3L0XA 1OK7A 4PNWA 2POLA 5AGUA 4TR8A 4N98A 3L0WA 4K3RA 4N9AA 4TSZA 3PWEA 4PNVA 4OVFA 4OVGA 4MJRA 3D1EA 4TRTA 5AH4A 1JQJA 3D1GA 4N95A 4MJQA 4N97A 5FVEA 4K74A 4K3MA 4K3PA 2AWAA 3Q4JA 4S3IA 5AH2A 4K3KA 4K3LA 4OVHA 4K3SA 4K3QA 3T0PA 1VPKA 3QSBB 2AVTA 5FRQA 1UNNA 3F1VA 4PNUA
chains in the Genus database with same CATH superfamily
1JQLA 3L10A 3P16A 3RB9A 3PGEB 3QSBA 2XURA 3Q4KA 3Q4LA 4K3OA 4N94A 3D1FA 1MMIA 3L0XB 4N99A 4N96A 4TR6A 4RKIA 4MJPA 3BEPA 4TR7A 3L0WB 5AGVA 3L0XA 3PGEA 1OK7A 4PNWA 2POLA 5AGUA 4TR8A 4N98A 3L0WA 4K3RA 4N9AA 4TSZA 3PWEA 4PNVA 4OVFA 4OVGA 4MJRA 3D1EA 4TRTA 5AH4A 1JQJA 3D1GA 4N95A 4MJQA 4N97A 5FVEA 4K74A 4K3MA 4K3PA 2AWAA 3Q4JA 4S3IA 5AH2A 4K3KA 4K3LA 3L10B 4K3SA 4K3QA 4OVHA 1VPKA 3T0PA 3QSBB 2AVTA 5FRQA 1UNNA 3F1VA 4PNUA
chains in the Genus database with same CATH topology
1JQLA 3L10A 3P16A 3RB9A 3PGEB 3QSBA 2XURA 3Q4KA 3Q4LA 4K3OA 4N94A 3D1FA 1MMIA 4N99A 4N96A 4TR6A 4RKIA 4MJPA 3BEPA 4TR7A 5AGVA 3L0XA 1OK7A 4PNWA 2POLA 5AGUA 4TR8A 4N98A 3L0WA 4K3RA 4N9AA 4TSZA 3PWEA 4PNVA 4OVFA 4OVGA 4MJRA 3D1EA 4TRTA 5AH4A 1JQJA 3D1GA 4N95A 4MJQA 4N97A 5FVEA 4K74A 4K3MA 4K3PA 2AWAA 3Q4JA 4S3IA 5AH2A 4K3KA 4K3LA 4OVHA 4K3SA 4K3QA 3T0PA 1VPKA 3QSBB 2AVTA 5FRQA 1UNNA 3F1VA 4PNUA
chains in the Genus database with same CATH homology


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