3BEPA

Structure of a sliding clamp on dna
Total Genus 92

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
92
sequence length
366
structure length
366
Chain Sequence
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL
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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
EMPTYS1 (2-6)S5 (63-64)AH1 (7-18)AH4 (197-206)TIV1 (18-21)3H1 (28-31)TVIII1 (25-28)S2 (32-38)AH2 (72-81)TI'1 (38-41)S3 (41-47)TIV2 (48-51)S4 (51-58)S17 (230-235)TII'4 (227-230)S6 (66-71)TII1 (83-86)S7 (87-93)TII'1 (93-96)S10 (124-131)AH3 (132-141)S12 (166-172)3H3 (143-145)S26 (357-361)3H4 (153-155)TIV4 (147-150)TIV5 (150-153)TIV6 (173-176)3H5 (244-246)S11 (157-163)S13 (176-183)AH6 (321-331)TVIII2 (355-358)S14 (191-196)TI1 (219-222)TIV7 (249-252)S18 (254-259)S22 (309-310)AH5 (260-272)S21 (301-307)TI2 (276-279)TIV8 (275-278)S19 (280-286)TII2 (286-289)S20 (289-295)TI3 (296-299)S23 (315-320)TI4 (342-345)S27 (363-364)S24 (335-340)TI5 (351-354)S25 (347-351)3H2 (113-115)TII'3 (163-166)S8 (96-101)S9 (104-109)S15 (213-219)S16 (222-227)Updating...
connected with : NaN
molecule tags Transferase, transcription/dna
source organism Escherichia coli
publication title Structure of a sliding clamp on DNA
pubmed doi rcsb
molecule keywords DNA (5'-D(P*DCP*DCP*DCP*DAP*DTP*DCP*DGP*DTP*DAP*DT)-3')
total genus 92
structure length 366
sequence length 366
chains with identical sequence B
ec nomenclature ec 2.7.7.7: DNA-directed DNA polymerase.
pdb deposition date 2007-11-19

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 3bepA02
3.10.150.10 Alpha Beta Roll DNA Polymerase III; Chain A, domain 2 DNA Polymerase III, subunit A, domain 2 3bepA03
3.10.150.10 Alpha Beta Roll DNA Polymerase III; Chain A, domain 2 DNA Polymerase III, subunit A, domain 2 3bepA01
4TRTA 3Q4LA 4RKIA 4TR8A 5FVEA 3L10A 2AWAA 3D1EA 4TSZA 4N94A 1VPKA 3BEPA 4K3PA 4OVGA 5AH4A 1JQJA 5FRQA 4K74A 1JQLA 3PWEA 3L0WA 3T0PA 4K3LA 2POLA 3RB9A 1OK7A 3PGEB 4N95A 5AGUA 3Q4KA 4N96A 5AH2A 4TR6A 4K3QA 4OVHA 5AGVA 2AVTA 3L0XA 3P16A 1UNNA 4N98A 3QSBA 4OVFA 4PNVA 3F1VA 4K3RA 4N99A 4K3KA 4TR7A 4PNWA 4K3MA 3QSBB 4MJRA 4MJQA 4K3OA 4S3IA 4K3SA 3D1FA 4MJPA 4PNUA 4N97A 1MMIA 2XURA 3D1GA 3Q4JA 4N9AA
chains in the Genus database with same CATH superfamily
4TRTA 3Q4LA 4RKIA 4TR8A 5FVEA 3L10A 2AWAA 3D1EA 4TSZA 4N94A 1VPKA 3BEPA 4K3PA 4OVGA 5AH4A 3L10B 1JQJA 5FRQA 4K74A 3PGEA 1JQLA 3PWEA 3L0WA 3T0PA 4K3LA 2POLA 3RB9A 1OK7A 3PGEB 3L0WB 4N95A 5AGUA 3Q4KA 4N96A 5AH2A 4TR6A 4K3QA 4OVHA 5AGVA 2AVTA 3L0XA 3P16A 1UNNA 4N98A 3QSBA 4OVFA 4PNVA 3F1VA 4K3RA 4N99A 4K3KA 4TR7A 3L0XB 4PNWA 4K3MA 3QSBB 4MJRA 4MJQA 4K3OA 4S3IA 4K3SA 3D1FA 4MJPA 4PNUA 4N97A 1MMIA 2XURA 3D1GA 3Q4JA 4N9AA
chains in the Genus database with same CATH topology
4TRTA 3Q4LA 4RKIA 4TR8A 5FVEA 3L10A 2AWAA 3D1EA 4TSZA 4N94A 1VPKA 3BEPA 4K3PA 4OVGA 5AH4A 1JQJA 5FRQA 4K74A 1JQLA 3PWEA 3L0WA 3T0PA 4K3LA 2POLA 3RB9A 1OK7A 3PGEB 4N95A 5AGUA 3Q4KA 4N96A 5AH2A 4TR6A 4K3QA 4OVHA 5AGVA 2AVTA 3L0XA 3P16A 1UNNA 4N98A 3QSBA 4OVFA 4PNVA 3F1VA 4K3RA 4N99A 4K3KA 4TR7A 4PNWA 4K3MA 3QSBB 4MJRA 4MJQA 4K3OA 4S3IA 4K3SA 3D1FA 4MJPA 4PNUA 4N97A 1MMIA 2XURA 3D1GA 3Q4JA 4N9AA
chains in the Genus database with same CATH homology


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