4N97 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   E. COLI SLIDING CLAMP IN COMPLEX WITH 5-NITROINDOLE

Authors :   Z. Yin, A. J. Oakley

Date :   19 Oct 13 (Deposition) - 06 Nov 13 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.97

Chains :   Asym./Biol. Unit : A,B

Keywords :   Sliding Clamp, Dnan, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Yin, L. R. Whittell, Y. Wang, S. Jergic, M. Liu, E. J. Harry, N. E. Dixon, J. L. Beck, M. J. Kelso, A. J. Oakley
Discovery Of Lead Compounds Targeting The Bacterial Sliding Clamp Using A Fragment-Based Approach.
J. Med. Chem. V. 57 2799 2014
PubMed-ID: 24592885 | Reference-DOI: 10.1021/JM500122R

Molecule 1 - DNA POLYMERASE III SUBUNIT BETA
	Chains	:	A, B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PND261
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B3701, DNAN, JW3678
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	BETA SLIDING CLAMP, BETA CLAMP

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	2HU	1	Ligand/Ion	5-NITRO-1H-INDOLE
2	CA	1	Ligand/Ion	CALCIUM ION
3	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:172 , GLY A:174 , HIS A:175 , VAL A:247 , SER A:346 , VAL A:360 , MET A:362 , HOH A:666 , HOH A:679	BINDING SITE FOR RESIDUE 2HU A 401
2	AC2	SOFTWARE	ARG A:105 , TYR A:284 , SER A:286 , GLN A:289 , HOH A:632	BINDING SITE FOR RESIDUE PEG A 402
3	AC3	SOFTWARE	LEU A:262 , ARG A:269 , HOH A:693 , HOH A:732 , HOH A:794 , HOH A:830 , PRO B:83	BINDING SITE FOR RESIDUE PEG A 403
4	AC4	SOFTWARE	TRP A:122 , GLN A:123 , SER A:124 , ARG A:224 , GLN B:36	BINDING SITE FOR RESIDUE PEG A 404
5	AC5	SOFTWARE	ARG A:103 , ARG A:105 , GLU B:303 , ILE B:305	BINDING SITE FOR RESIDUE CA A 405
6	AC6	SOFTWARE	GLU A:303 , ARG B:105 , GLN B:289	BINDING SITE FOR RESIDUE PEG B 401

(no "SS Bond" information available for 4N97)

(no "Cis Peptide Bond" information available for 4N97)

(no "SAP(SNP)/Variant" information available for 4N97)

(no "PROSITE Motif" information available for 4N97)

(no "Exon" information available for 4N97)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4n97a1 A:1-122 DNA polymerase III, beta subunit                                                                     d4n97a2 A:123-244 DNA polymerase III, beta subunit                                                                        d4n97a3 A:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhh...hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhh......eeeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhhhh.....eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n97 A   1 MKFTVEREHLLKPLQQVSGPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20|       35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365 
                                              20|                                                                                                                                                                                                                                                                                                                                                    
                                               26

Chain B from PDB  Type:PROTEIN  Length:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4n97b1 B:1-122 DNA polymerase III, beta subunit                                                                         d4n97b2 B:123-244 DNA polymerase III, beta subunit                                                                        d4n97b3 B:245-365 DNA polymerase III, beta subunit                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh......hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeee...eeeeehhhhhhhhhh.......eeeee...eeeeee..eeeeee..................eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n97 B   1 MKFTVEREHLLKPLQQVSGPLGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMR 365
                                    10        20||      31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
                                               21|                                                                                                                                                                                                                                                                                                                                                      
                                                23

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: DNA clamp (88)

Superfamily: DNA clamp (88)

Family: DNA polymerase III, beta subunit (31)

Protein domain: DNA polymerase III, beta subunit (31)

Escherichia coli [TaxId: 562] (30)

1a	d4n97a1	A:1-122
1b	d4n97a2	A:123-244
1c	d4n97a3	A:245-366
1d	d4n97b1	B:1-122
1e	d4n97b2	B:123-244
1f	d4n97b3	B:245-365

(no "CATH Domain" information available for 4N97)

(no "Pfam Domain" information available for 4N97)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4n97)

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	4n97
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		Orientation in Membranes	:	OPM
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	DPO3B_ECOLI \| P0A988
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	2.7.7.7
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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