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Asym./Biol. Unit (Jmol Viewer)

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Title :   E. COLI SLIDING CLAMP IN COMPLEX WITH (R)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-2-CARBOXYLIC ACID

Authors :   Z. Yin, A. J. Oakley

Date :   21 Feb 14 (Deposition) - 05 Mar 14 (Release) - 24 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Poliii Beta, Sliding Clamp, Dnan, Transferase, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Yin, L. R. Whittell, Y. Wang, S. Jergic, C. Ma, P. J. Lewis, N. E. Dixon J. L. Beck, M. J. Kelso, A. J. Oakley
Bacterial Sliding Clamp Inhibitors That Mimic The Sequentia Binding Mechanism Of Endogenous Linear Motifs.
J. Med. Chem. V. 58 4693 2015
PubMed-ID: 25970224 | Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00232

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 Strain	:	AN1459
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BN896_3391, DNAN
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	1403831
	Strain	:	K-12 SUBSTR. MC4100

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 14)

No.	Name	Count	Type	Full Name
1	2VG	2	Ligand/Ion	(2R)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-2-CARBOXYLIC ACID
2	CA	4	Ligand/Ion	CALCIUM ION
3	CL	1	Ligand/Ion	CHLORIDE ION
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:9 , THR A:41 , ARG A:56 , ALA A:58 , ASP A:229 , HOH A:597	BINDING SITE FOR RESIDUE PG4 A 401
02	AC2	SOFTWARE	ALA A:86 , GLU A:87 , ALA A:89 , SER A:101 , GLY A:102 , HOH A:752	BINDING SITE FOR RESIDUE PEG A 402
03	AC3	SOFTWARE	THR A:129 , PRO A:131 , GLN A:132 , ASP A:211 , ASN A:212 , PRO A:213 , HOH A:602	BINDING SITE FOR RESIDUE PEG A 403
04	AC4	SOFTWARE	ASP A:121 , TRP A:122 , SER A:124 , ARG A:224 , HOH A:709 , ALA B:38 , HOH B:625	BINDING SITE FOR RESIDUE PG4 A 404
05	AC5	SOFTWARE	ASN A:251 , HOH A:717 , HOH A:762 , HOH B:718	BINDING SITE FOR RESIDUE CA A 405
06	AC6	SOFTWARE	GLY A:280 , ALA A:294 , ASN A:295 , HOH A:637 , HOH A:671	BINDING SITE FOR RESIDUE CA A 406
07	AC7	SOFTWARE	ARG A:152 , TYR A:154 , THR A:172 , GLY A:174 , ARG A:176 , LEU A:177 , PRO A:242 , VAL A:247 , MET A:362 , HOH A:774	BINDING SITE FOR RESIDUE 2VG A 407
08	AC8	SOFTWARE	GLY B:280 , ALA B:294 , ASN B:295 , HOH B:609 , HOH B:758	BINDING SITE FOR RESIDUE CA B 401
09	AC9	SOFTWARE	GLU B:161 , THR B:162 , SER B:190	BINDING SITE FOR RESIDUE CA B 402
10	BC1	SOFTWARE	ALA A:38 , TRP B:122 , ARG B:224 , HOH B:634 , HOH B:652 , HOH B:702	BINDING SITE FOR RESIDUE PG4 B 403
11	BC2	SOFTWARE	LYS A:250 , SER A:345 , HOH A:550 , GLU B:163 , GLU B:166 , ARG B:168 , SER B:181 , MET B:182 , PRO B:183 , HOH B:624 , HOH B:671 , HOH B:679 , HOH B:738	BINDING SITE FOR RESIDUE PGE B 404
12	BC3	SOFTWARE	ARG B:152 , TYR B:154 , THR B:172 , GLY B:174 , HIS B:175 , ARG B:176 , LEU B:177 , HOH B:641 , HOH B:650	BINDING SITE FOR RESIDUE 2VG B 405
13	BC4	SOFTWARE	ALA B:258 , GLY B:259 , LEU B:262 , ASP B:307 , VAL B:308 , THR B:309 , ASN B:335 , HOH B:613 , HOH B:648	BINDING SITE FOR RESIDUE PGE B 406

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:19	-	Pro A:20
2	Leu A:207	-	Asp A:208

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

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

(no "Exon" information available for 4OVF)

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:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4ovfa1 A:1-122 DNA polymerase III, beta subunit                                                                      d4ovfa2 A:123-244 DNA polymerase III, beta subunit                                                                        d4ovfa3 A:245-364 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.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhh...eeeeee......eeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ovf A   1 MKFTVEREHLLKPLQQVSGPPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPM 364
                                    10        20|       34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364
                                              20|                                                                                                                                                                                                                                                                                                                                                   
                                               25

Chain B from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4ovfb1 B:1-122 DNA polymerase III, beta subunit                                                                  d4ovfb2 B:123-244 DNA polymerase III, beta subunit                                                                        d4ovfb3 B:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhhh......eeeee...eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ovf B   1 MKFTVEREHLLKPLQQVSLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10       |28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358        
                                            18|                                                                                                                                                                                                                                                                                                                                                   
                                             27

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	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	d4ovfa1	A:1-122
1b	d4ovfa2	A:123-244
1c	d4ovfa3	A:245-364
1d	d4ovfb1	B:1-122
1e	d4ovfb2	B:123-244
1f	d4ovfb3	B:245-366

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

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

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4OVF)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:19 - Pro A:20	[ RasMol ]
		Leu A:207 - Asp A:208	[ RasMol ]

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Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (6, 14)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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