4N98 | Genus

Total Genus 84

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	84
sequence length	364
structure length	358
Chain Sequence	MKFTVEREHLLKPLQQVSGTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPM

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/5d00806d3665ad2917effe02/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d00806d3665ad2917effe02/pdb.gz): 1209 ms

reading 358 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

358 atoms created

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

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:357});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	Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. pubmed doi rcsb
molecule keywords	DNA polymerase III subunit beta
molecule tags	Transferase/transferase inhibitor
source organism	Escherichia coli
total genus	84
structure length	358
sequence length	364
chains with identical sequence	B
ec nomenclature	ec 2.7.7.7: DNA-directed DNA polymerase.
pdb deposition date	2013-10-19

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	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	4n98A02
3.10.150.10	Alpha Beta	Roll	DNA Polymerase III; Chain A, domain 2	DNA Polymerase III, subunit A, domain 2	4n98A03
3.10.150.10	Alpha Beta	Roll	DNA Polymerase III; Chain A, domain 2	DNA Polymerase III, subunit A, domain 2	4n98A01

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

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

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

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#similar chains, but unknotted
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4N98A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations